The coupled-cluster description of electronic structure: perspectives for bioinorganic chemistry

This commentary provides an overview of the challenges and strengths of coupled-cluster theory when applied to active sites of metalloproteins. It is argued that thanks to increases in computer power and remarkable methodological developments, coupled-cluster methods will make increasingly important contributions to understanding the structure, properties and reactivity of transition metal cofactors.

Cold chemistry with electronically excited Ca+ Coulomb crystals

Rate constants for chemical reactions of laser-cooled Ca(+) ions and neutral polar molecules (CH(3)F, CH(2)F(2), or CH(3)Cl) have been measured at low collision energies (<E(coll)>/k(B)=5-243 K). Low kinetic energy ensembles of (40)Ca(+) ions are prepared through Doppler laser cooling to form "Coulomb crystals" in which the ions form a latticelike arrangement in the trapping potential. The trapped ions react with translationally cold beams of polar molecules produced by a quadrupole guide velocity selector or with room-temperature gas admitted into the vacuum chamber. Imaging of the Ca(+) ion fluorescence allows the progress of the reaction to be monitored. Product ions are sympathetically cooled into the crystal structure and are unambiguously identified through resonance-excitation mass spectrometry using just two trapped ions. Variations of the laser-cooling parameters are shown to result in different steady-state populations of the electronic states of (40)Ca(+) involved in the laser-cooling cycle, and these are modeled by solving the optical Bloch equations for the eight-level system. Systematic variation of the steady-state populations over a series of reaction experiments allows the extraction of bimolecular rate constants for reactions of the ground state ((2)S(1/2)) and the combined excited states ((2)D(3/2) and (2)P(1/2)) of (40)Ca(+). These results are analyzed in the context of capture theories and ab initio electronic structure calculations of the reaction profiles. In each case, suppression of the ground state rate constant is explained by the presence of a submerged or real barrier on the ground state potential surface. Rate constants for the excited states are generally found to be in line with capture theories.

Analysis of chorismate mutase catalysis by QM/MM modelling of enzyme-catalysed and uncatalysed reactions

Chorismate mutase is at the centre of current controversy about fundamental features of biological catalysts. Some recent studies have proposed that catalysis in this enzyme does not involve transition state (TS) stabilization but instead is due largely to the formation of a reactive conformation of the substrate. To understand the origins of catalysis, it is necessary to compare equivalent reactions in different environments. The pericyclic conversion of chorismate to prephenate catalysed by chorismate mutase also occurs (much more slowly) in aqueous solution. In this study we analyse the origins of catalysis by comparison of multiple quantum mechanics/molecular mechanics (QM/MM) reaction pathways at a reliable, well tested level of theory (B3LYP/6-31G(d)/CHARMM27) for the reaction (i) in Bacillus subtilis chorismate mutase (BsCM) and (ii) in aqueous solvent. The average calculated reaction (potential energy) barriers are 11.3 kcal mol(-1) in the enzyme and 17.4 kcal mol(-1) in water, both of which are in good agreement with experiment. Comparison of the two sets of reaction pathways shows that the reaction follows a slightly different reaction pathway in the enzyme than in it does in solution, because of a destabilization, or strain, of the substrate in the enzyme. The substrate strain energy within the enzyme remains constant throughout the reaction. There is no unique reactive conformation of the substrate common to both environments, and the transition state structures are also different in the enzyme and in water. Analysis of the barrier heights in each environment shows a clear correlation between TS stabilization and the barrier height. The average differential TS stabilization is 7.3 kcal mol(-1) in the enzyme. This is significantly higher than the small amount of TS stabilization in water (on average only 1.0 kcal mol(-1) relative to the substrate). The TS is stabilized mainly by electrostatic interactions with active site residues in the enzyme, with Arg90, Arg7 and Glu78 generally the most important. Conformational effects (e.g. strain of the substrate in the enzyme) do not contribute significantly to the lower barrier observed in the enzyme. The results show that catalysis is mainly due to better TS stabilization by the enzyme.

Diabetes, metformin and lactic acidosis

OBJECTIVE

Metformin has long been thought to cause lactic acidosis (LA) but evidence from various sources has led researchers to question a direct causative relationship. We assessed the relationship of metformin prescription and other factors to the incidence of LA.

METHODS

All cases of LA at a single hospital were identified from laboratory lactate measurements. We compared patients classified as Cohen and Woods class A and B, patients with and without diabetes, and those taking metformin or not.

RESULTS

LA was more common than in published analyses based on hospital coding of diagnoses. The incidence of LA was greater in diabetes than in the nondiabetic population but with no further increase in patients taking metformin. Lactate levels were no greater in patients on metformin than in patients with type 2 diabetes not on metformin even if patients with acute cardiorespiratory disturbance (Cohen and Woods class A) were excluded. Acidosis was greater in diabetes (hydrogen ion 94·9 ± 4·6 vs 83·2 ± 2·3 10(-9) m, P = 0·027) but factors besides lactate contributed. Acute cardiorespiratory illness, acute renal impairment and sepsis were the most common of the recognized precipitating factors. Age (P = 0·01), acute renal failure (P = 0·015) and sepsis (P = 0·005) were associated with mortality.

CONCLUSIONS

Diabetes rather than metformin therapy is the major risk factor for the development of LA. Lactic acidosis occurs in association with acute illness particularly in diabetes. Current guidance for the prevention of lactic acidosis may overemphasize the role of metformin.

Accuracy in determining interproton distances using Nuclear Overhauser Effect data from a flexible molecule

The determination of accurate NOE-derived interproton distances and confirmation/prediction of relative populations in multi-conformer, flexible small molecules was investigated with the model compound 4-propylaniline. The low accuracy assumed for semi-quantitative NOE distance restraints is typically taken to suggest that large numbers of constraints need to be used in the dynamical analysis of flexible molecules, and this requires, for example, the measurement and Karplus-type analysis of scalar coupling constants ((3)J(CH) and (3)J(HH)). Herein we demonstrate that, contrary to this common perception, NOE measurements alone are accurate enough to establish interproton distances, and hence conformational detail, in flexible molecules to within a few percent of their ensemble-averaged values, hence reducing the demand for additional restraints in such dynamic analyses.

CH2 group migration between the H-terminated 2×1 reconstructed {100} and {111} surfaces of diamond

Various possible routes for the migration of a CH2 group between the H-terminated 2×1 reconstructed {100} surface and the H-terminated {111} surface of diamond have been explored using a hybrid quantum mechanical/molecular mechanical method. The calculated energies suggest that movement of such surface bound species across step edges should be a facile process under typical diamond growth conditions, and that such migrations are significant contributors to the observed morphologies of diamond grown by chemical vapor deposition methods.

Testing high-level QM/MM methods for modeling enzyme reactions: acetyl-CoA deprotonation in citrate synthase

Combined quantum mechanics/molecular mechanics (QM/MM) calculations with high levels of correlated ab initio theory can now provide benchmarks for enzyme-catalyzed reactions. Here, we use such methods to test various QM/MM methods and the sensitivity of the results to details of the models for an important enzyme reaction, proton abstraction from acetyl-coenzyme A in citrate synthase. We calculate multiple QM/MM potential energy surfaces up to the local coupled cluster theory (LCCSD(T0)) level, with structures optimized at hybrid density functional theory and Hartree-Fock levels. The influence of QM methods, basis sets, and QM region size is shown to be significant. Correlated ab initio QM/MM calculations give barriers in agreement with experiment for formation of the acetyl-CoA enolate intermediate. In contrast, B3LYP fails to identify the enolate as an intermediate, whereas BH&HLYP does. The results indicate that QM/MM methods and setup should be tested, ideally using high-level calculations, to draw reliable mechanistic conclusions.

Design of an infrared laser pulse to control the multiphoton dissociation of the Fe-CO bond in CO-heme compounds

Optimal control theory is used to design a laser pulse for the multiphoton dissociation of the Fe-CO bond in the CO-heme compounds. The study uses a hexacoordinated iron-porphyrin-imidazole-CO complex in its ground electronic state as a model for CO liganded to the heme group. The potential energy and dipole moment surfaces for the interaction of the CO ligand with the heme group are calculated using density functional theory. Optimal control theory, combined with a time-dependent quantum dynamical treatment of the laser-molecule interaction, is then used to design a laser pulse capable of efficiently dissociating the CO-heme complex model. The genetic algorithm method is used within the mathematical framework of optimal control theory to perform the optimization process. This method provides good control over the parameters of the laser pulse, allowing optimized pulses with simple time and frequency structures to be designed. The dependence of photodissociation yield on the choice of initial vibrational state and of initial laser field parameters is also investigated. The current work uses a reduced dimensionality model in which only the Fe-C and C-O stretching coordinates are explicitly taken into account in the time-dependent quantum dynamical calculations. The limitations arising from this are discussed in Sec. IV.