Ian H. Williams

Use and abuse of the distinguished-coordinate method for transition-state structure searching

Abstract Exploration of potential-energy surfaces for reacting systems is often expedited by selection of a distinguished coordinate, to measure progress between reactants and products, at each value of which the remaining coordinates are optimized by constrained energy-minimization. A classification of surfaces is suggested according to the number of energy minima in the subspace excluding the distinguished coordinate in the saddle region. Type S surfaces are well behaved in the distinguished-coordinate method but type D surfaces are not. In general, reaction paths and energy profiles generated by this method for type D surfaces are discontinuous and cannot be used to locate transition-state structures precisely. An extension of the method using two distinguished coordinates is discussed in relation to the example of formaldehyde hydration but is found to suffer from the same pathological condition in two dimensions as does the standard method in one dimension.

Transition-state structural refinement with GRACE and CHARMM: Flexible QM/MM modelling for lactate dehydrogenase

Realistic simulations of chemical reactions require the use not only of methods capable of describing accurately the energy of molecules undergoing bonding changes within a particular chemical environment, but also of methods capable of exploring topographical features of significance on energy hypersurfaces spanning perhaps several thousand degrees of freedom. Hybrid quantum-mechanical/molecular-mechanical techniques show much promise for the first task, but existing computer codes are inadequate for the second. Application of these methods to real chemical problems demands new tools for location and characterisation of saddle-points, intrinsic reaction coordinates, hessians and vibrational frequencies for very large flexible systems. Algorithms capable of performing these tasks have been incorporated in a new software package, GRACE, which provides a non-invasive interface between popular codes for quantum chemistry and molecular dynamics and modelling. Transition structures (TSs) have been refined by this novel procedure, using a combined AM1/CHARMM24/TIP3P potential, involving full gradient relaxation of the positions of 1900–2000 atoms of a solvated enzyme–substrate complex (lactate dehydrogenase/NADH/pyruvate/water). Six different starting structures (arbitrarily selected from a molecular dynamics trajectory for the enzyme–substrate complex) lead to six different TSs. Although the essential features of these TSs are invariant, the relative dispositions of active-site residues differ quite significantly. The transition state for the enzymic reaction would represent an average of the properties of many, nearly degenerate TSs. This insight emerges only as a consequence of the flexible model of the active site employed in this study.

On the representation of force fields for chemically reacting systems

Abstract “Relaxed” force constants are uniquely defined for systems involving redundant coordinates, in contradistinction to the usual “rigid” force constants, and thus their use allows meaningful correlations to be made between force fields calculated for reactants, transition state, and product of a chemical reaction, for example formaldehyde hydration.

Pressure dependence and metastable state formation in the photolysis of dichlorine monoxide (Cl2O)

The photodissociation of dichlorine monoxide (Cl2O) was studied using broadband flash photolysis to investigate the influence of variations in the photolysis wavelength domain, bath gas pressure and bath gas identity on the yield and temporal dependence of the ClO product. ClO yields were independent of bath gas pressure when the photolysis spectral band extended to 200 nm (quartz cutoff) but for photolysis restricted to wavelengths longer than about 250 nm, ClO yields decreased with increasing bath gas pressure and there was a pressure‐dependent delay in the formation of ClO. Under these conditions, a weak, highly structured absorption spectrum was observed in the range 16 600–26 000 cm−1 with a lifetime on the order of 500 ms. A portion of the spectrum could be analyzed (22 000–26 000 cm−1) which showed progressions having differences of 283, 443, and 505 cm−1. Ab initio calculations were performed to evaluate vertical excitation energies and oscillator strengths from the lowest‐energy singlet (X 1A1) o...

Dissociation dynamics of FCO and HCO radicals

Dissociation energies and barriers to dissociation for XCO→X+CO have been calculated for X 2A’ and A 2π states of FCO and HCO by ab initio molecular orbital methods. At the PUMP4//UMP2/6‐311G* level, D○298 (F‐CO)=22.3 kcal mol−1 and ΔH298=24.2 kcal mol−1 for dissociation of ground‐state FCO; these values are much higher than the corresponding bond energy and activation enthalpy for HCO dissociation. Calculated RRKM rate constants suggests that the lifetime of FCO under stratospheric conditions is sufficient to allow bimolecular reactions to compete with dissociation. Reaction with O2 may provide an in situ source of stratospheric CO2.

Computational mutagenesis reveals the role of active-site tyrosine in stabilising a boat conformation for the substrate: QM/MM molecular dynamics studies of wild-type and mutant xylanases

Molecular dynamics simulations have been performed for non-covalent complexes of phenyl beta-xylobioside with the retaining endo-beta-1,4-xylanase from B. circulans (BCX) and its Tyr69Phe mutant using a hybrid QM/MM methodology. A trajectory initiated for the wild-type enzyme-substrate complex with the proximal xylose ring bound at the -1 subsite (adjacent to the scissile glycosidic bond) in the (4)C(1) chair conformation shows spontaneous transformation to the (2,5)B boat conformation, and potential of mean force calculations indicate that the boat is approximately 30 kJ mol(-1) lower in free energy than the chair. Analogous simulations for the mutant lacking one oxygen atom confirm the key role of Tyr69 in stabilizing the boat in preference to the (4)C(1) chair conformation, with a relative free energy difference of about 20 kJ mol(-1), by donating a hydrogen bond to the endocyclic oxygen of the proximal xylose ring. QM/MM MD simulations for phenyl beta-xyloside in water, with and without a propionate/propionic acid pair to mimic the catalytic glutamate/glutamic acid pair of the enzyme, show the (4)C(1) chair to be stable, although a hydrogen bond between the OH group at C2 of xylose and the propionate moiety seems to provide some stabilization for the (2,5)B conformation.

Probing Synergy between Two Catalytic Strategies in the Glycoside Hydrolase O-GlcNAcase Using Multiple Linear Free Energy Relationships

Human O-GlcNAcase plays an important role in regulating the post-translational modification of serine and threonine residues with beta-O-linked N-acetylglucosamine monosaccharide unit (O-GlcNAc). The mechanism of O-GlcNAcase involves nucleophilic participation of the 2-acetamido group of the substrate to displace a glycosidically linked leaving group. The tolerance of this enzyme for variation in substrate structure has enabled us to characterize O-GlcNAcase transition states using several series of substrates to generate multiple simultaneous free-energy relationships. Patterns revealing changes in mechanism, transition state, and rate-determining step upon concomitant variation of both nucleophilic strength and leaving group abilities are observed. The observed changes in mechanism reflect the roles played by the enzymic general acid and the catalytic nucleophile. Significantly, these results illustrate how the enzyme synergistically harnesses both modes of catalysis; a feature that eludes many small molecule models of catalysis. These studies also suggest the kinetic significance of an oxocarbenium ion intermediate in the O-GlcNAcase-catalyzed hydrolysis of glucosaminides, probing the limits of what may be learned using nonatomistic investigations of enzymic transition-state structure and offering general insights into how the superfamily of retaining glycoside hydrolases act as efficient catalysts.

Mechanism of glycoside hydrolysis: A comparative QM/MM molecular dynamics analysis for wild type and Y69F mutant retaining xylanases

Computational simulations have been performed using hybrid quantum-mechanical/molecular-mechanical potentials to investigate the catalytic mechanism of the retaining endo-beta-1, 4-xylanase (BCX) from B. circulans. Two-dimensional potential-of-mean-force calculations based upon molecular dynamics with the AM1/OPLS method for wild-type BCX with a p-nitrophenyl xylobioside substrate in water clearly indicates a stepwise mechanism for glycosylation: the rate-determining step is nucleophilic substitution by Glu78 to form the covalently bonded enzyme-substrate intermediate without protonation of the leaving group by Glu172. The geometrical configuration of the transition state for the enzymic reaction is essentially the same as found for a gas-phase model involving only the substrate and a propionate/propionic acid pair to represent the catalytic glutamate/glutamic acid groups. In addition to stabilizing the (2,5)B boat conformation of the proximal xylose in the non-covalent reactant complex of the substrate with BCX, Tyr69 lowers the free-energy barrier for glycosylation by 42 kJ mol(-1) relative to that calculated for the Y69F mutant, which lacks the oxygen atom O(Y). B3LYP/6-31+G* energy corrections reduce the absolute height of the barrier to reaction. In the oxacarbenium ion-like transition state O(Y) approaches closer to the endocyclic oxygen O(ring) of the sugar ring but donates its hydrogen bond not to O(ring) but rather to the nucleophilic oxygen of Glu78. Comparison of the average atomic charge distributions for the wild-type and mutant indicates that charge separation along the bond between the anomeric carbon and O(ring) is matched in the former by a complementary separation of charge along the O(Y)-H(Y) bond, corresponding to a pair of roughly antiparallel bond dipoles, which is not present in the latter.

High-level ab initio studies of the structure, vibrational spectra, and energetics of S3

Observation of mass-dependent and non-mass-dependent sulfur isotope fractionations in elemental sulfur is providing new insight into the nature of the sulfur cycle in the atmosphere. Interpretation of the experimental isotope data requires estimation of the energetics for the reaction S+S2-->S3 (isoelectronic with O+O2-->O3). Key molecular properties of the S3 potential-energy surface, such as vibrational frequencies and isotopic shifts, are presented that can be used to assess the mass-dependent fractionation effect. Ab initio results are compared to the available experimental results for S2 to evaluate the reliability of the computational results for S3. The S-S bond dissociation energy for S3 is determined to be 60.9+/-1 kcal mol(-1).

Dissociation dynamics of the trifluoromethoxy radical

Abstract Trifluoromethoxy radical formation (by O-atom addition to trifluoromethyl) and dissociation (by F-atom elimination) are studied by ab initio molecular-orbital theory. The activation enthalpy (298 K) for F-atom elimination is 35.3 kcal mol−1 at the UMP4SDQ/6-31 G∗//UHF/6-31 G∗+ΔZPE+Δ(H-E0 level. The implication of calculated RRKM dissociation rate constants is discussed.