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Richard A Friesner

Publications and source records attributed to Richard A Friesner.

16 recordsLinked to original sources
PubMed2003

Kinetics and thermodynamics of H. transfer from (eta5-C5R5)Cr(CO)3H (R = Ph, Me, H) to methyl methacrylate and styrene.

The rates of H/D exchange have been measured between (a) the activated olefins methyl methacrylate-d(5) and styrene-d(8), and (b) the Cr hydrides (eta(5)-C(5)Ph(5))Cr(CO)(3)H (2a), (eta(5)-C(5)Me(5))Cr(CO)(3)H (2b), and (eta(5)-C(5)H(5))Cr(CO)(3)H (2c). With a large excess of the deuterated olefin the first exchange goes to completion before subsequent exchanges begin, at a rate first order in olefin and in hydride. (Hydrogenation is insignificant except with styrene and CpCr(CO)(3)H; in most cases, the radicals arising from the first H. transfer are too hindered to abstract another H. .) Statistical corrections give the rate constants k(reinit) for H. transfer to the olefin from the hydride. With MMA, k(reinit) decreases substantially as the steric bulk of the hydride increases; with styrene, the steric bulk of the hydride has little effect. At longer times, the reaction of MMA or styrene with 2a gives the corresponding metalloradical 1a as termination depletes the concentration of the methyl isobutyryl radical 3 or the alpha-methylbenzyl radical 4; computer simulation of [1a] as f(t) gives an estimate of k(tr), the rate constant for H. transfer from 3 or 4 back to Cr. These rate constants imply a DeltaG (50 degrees C) of +11 kcal/mol for H. transfer from 2a to MMA, and a DeltaG (50 degrees C) of +10 kcal/mol for H. transfer from 2a to styrene. The CH(3)CN pK(a) of 2a, 11.7, implies a BDE for its Cr-H bond of 59.6 kcal/mol, and DFT calculations give 58.2 kcal/mol for the Cr-H bond in 2c. In combination the kinetic DeltaG values, the experimental BDE for 2a, and the calculated DeltaS values for H. transfer imply a C-H BDE of 45.6 kcal/mol for the methyl isobutyryl radical 3 (close to the DFT-calculated 49.5 kcal/mol), and a C-H BDE of 47.9 kcal/mol for the alpha-methylbenzyl radical 4 (close to the DFT-calculated 49.9 kcal/mol). A solvent cage model suggests 46.1 kcal/mol as the C-H BDE for the chain-carrying radical in MMA polymerization.

Chromium↗
PubMed2003

Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450.

We elucidate the hydroxylation of camphor by cytochrome P450 with the use of density functional and mixed quantum mechanics/molecular mechanics methods. Our results reveal that the enzyme catalyzes the hydrogen-atom abstraction step with a remarkably low free-energy barrier. This result provides a satisfactory explanation for the experimental failure to trap the proposed catalytically competent high-valent heme Fe(IV) oxo (oxyferryl) species responsible for this hydroxylation chemistry. The primary and previously unappreciated contribution to stabilization of the transition state is the interaction of positively charged residues in the active-site cavity with carboxylate groups on the heme periphery. A similar stabilization found in dioxygen binding to hemerythrin, albeit with reversed polarity, suggests that this mechanism for controlling the relative energetics of redox-active intermediates and transition states in metalloproteins may be widespread in nature.

Camphor↗
PubMed2003

Reversible dioxygen binding to hemerythrin.

A combination of conventional quantum chemical methods and a recently developed mixed quantum mechanical/molecular mechanical (QM/MM) method (QSite) is used to determine the different energetic components involved in reversible binding of O(2) to hemerythrin. The use of an accurate quantum chemical description of the active site and the inclusion of effects from the surrounding protein environment are both essential to achieve reversibility and thus to model accurately the binding of O(2) to the carboxylate-bridged diiron center in the protein. The major contributions from the protein environment stabilizing dioxygen binding are (1) the van der Waals interaction between the bound dioxygen and the protein atoms and (2) an increase in the hydrogen bonding energy of an imidazole group, ligated to one of the iron atoms, and a neighboring carboxylate side chain in the second coordination sphere. The protein strain energy for this system is negligible. The calculated total O(2) binding free energy is in good agreement with that derived from the experimental equilibrium constant.

Hemerythrin↗
PubMed2003

A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations.

We present an approximation, which allows reduction of computational resources needed to explicitly incorporate electrostatic polarization into molecular simulations utilizing empirical force fields. The proposed method is employed to compute three-body energies of molecular complexes with dipolar electrostatic probes, gas-phase dimerization energies, and pure liquid properties for five systems that are important in biophysical and organic simulations-water, methanol, methylamine, methanethiol, and acetamide. In all the cases, the three-body energies agreed with high level ab initio data within 0.07 kcal/mol, dimerization energies-within 0.43 kcal/mol (except for the special case of the CH(3)SH), and computed heats of vaporization and densities differed from the experimental results by less than 2%. Moreover, because the presented method allows a significant reduction in computational cost, we were able to carry out the liquid-state calculations with Monte Carlo technique. Comparison with the full-scale point dipole method showed that the computational time was reduced by 3.5 to more than 20 times, depending on the system in hand and on the desired level of the full-scale model accuracy, while the difference in energetic results between the full-scale and the presented approximate model was not great in the most cases. Comparison with the nonpolarizable OPLS-AA force field for all the substances involved and with the polarizable POL3 and q90 models for water and methanol, respectively, demonstrates that the presented technique allows reduction of computational cost with no sacrifice of accuracy. We hope that the proposed method will be of benefit to research employing molecular modeling technique in the biophysical and physical organic chemistry areas.

Algorithms↗
PubMed2002

Hydroxylation of methane by non-heme diiron enzymes: molecular orbital analysis of C-H bond activation by reactive intermediate Q.

The electronic structures of key species involved in methane hydroxylation performed by the hydroxylase component of soluble methane monooxygenase (sMMO), as proposed previously on the basis of high-level density functional theory, were investigated. The reaction starts with initial approach of methane at one of the bridging oxo atoms in intermediate Q, a di(mu-oxo)diiron(IV) unit. This step is accompanied by a proton-coupled outer-sphere transfer of the first electron from a C-H sigma-bond in methane to one of the metal centers. The second electron transfer, also an outer-sphere electron transfer process, occurs along a two-component reaction pathway. Both redox reactions are strongly coupled to structural distortions of the diiron core. The electronic consequence and driving force of these distortions are intuitively explained by using the computed Kohn-Sham orbitals in the broken-symmetry framework to incorporate the experimentally observed antiferromagnetic coupling of the unpaired electrons at the metal centers. The broken-symmetry orbital scheme is essential for describing the C-H bond activation process in a consistent and complete manner, enabling derivation of both an intuitive and quantitative understanding of the most salient electronic features that govern the details of the hydroxylation.

Electrons↗
PubMed2002

A non-classical hydrogen bond in the molybdenum arene complex [eta 6-C6H5C6H3(Ph)OH]Mo(PMe3)3: evidence that hydrogen bonding facilitates oxidative addition of the O-H bond.

Mo(PMe3)6 reacts with 2,6-Ph2C6H3OH to give the eta 6-arene complex [eta 6-C6H5C6H3(Ph)OH]Mo(PMe3)3 which exhibits a non-classical Mo...H-OAr hydrogen bond; DFT calculations indicate that the hydrogen bonding interaction facilitates oxidative addition of the O-H bond to give [eta 6,eta 1-C6H5C6H3(Ph)O]Mo(PMe3)2H.

Electrochemistry↗
PubMed2002

Ab initio quantum calculation of the diabatic coupling matrix elements for the self-exchange redox couples M(Cp)20/+ (M = Fe, Co; Cp = C5H5).

The diabatic couplings between the metal centers in M(Cp)20/+ (M = Fe, Co; Cp = C5H5) were evaluated using ab initio methods at the Hartree-Fock level of theory. Excellent agreement with the experimental estimate is found for the Fe(Cp)20/+ couple. For Co(Cp)20/+, the calculated numbers are substantially higher than the experimental estimates, suggesting that the latter may represent a considerable underestimate (a possibility mentioned in the experimental publication).

Journal Article↗
PubMed2002

A novel fold recognition method using composite predicted secondary structures.

In this work, we introduce a new method for fold recognition using composite secondary structures assembled from different secondary structure prediction servers for a given target sequence. An automatic, complete, and robust way of finding all possible combinations of predicted secondary structure segments (SSS) for the target sequence and clustering them into a few flexible clusters, each containing patterns with the same number of SSS, is developed. This program then takes two steps in choosing plausible homologues: (i) a SSS-based alignment excludes impossible templates whose SSS patterns are very different from any of those of the target; (ii) a residue-based alignment selects good structural templates based on sequence similarity and secondary structure similarity between the target and only those templates left in the first stage. The secondary structure of each residue in the target is selected from one of the predictions to find the best match with the template. Truncation is applied to a target where different predictions vary. In most cases, a target is also divided into N-terminal and C-terminal fragments, each of which is used as a separate subsequence. Our program was tested on the fold recognition targets from CASP3 with known PDB codes and some available targets from CASP4. The results are compared with a structural homologue list for each target produced by the CE program (Shindyalov and Bourne, Protein Eng 1998;11:739-747). The program successfully locates homologues with high Z-score and low root-mean-score deviation within the top 30-50 predictions in the overwhelming majority of cases.

Algorithms↗
PubMed2002

Reactions of methane monooxygenase intermediate Q with derivatized methanes.

The reactivity of intermediate Q of soluble methane monooxygenase from Methylococcus capsulatus (Bath) with a series of derivatized methanes of general formula CH3-R, where R = CN, NO2, and OH, and their deuterated analogues is described. Despite relatively slow reactions, significant kinetic isotope effects, KIEs, are observed in reactions with acetonitrile and nitromethane; however, none is obtained with methanol. In addition, evidence of a substrate-binding step that occurs prior to substrate oxidation is observed.

Kinetics↗
PubMed2002

On the role of the crystal environment in determining protein side-chain conformations.

The role of crystal packing in determining the observed conformations of amino acid side-chains in protein crystals is investigated by (1) analysis of a database of proteins that have been crystallized in different unit cells (space group or unit cell dimensions) and (2) theoretical predictions of side-chain conformations with the crystal environment explicitly represented. Both of these approaches indicate that the crystal environment plays an important role in determining the conformations of polar side-chains on the surfaces of proteins. Inclusion of the crystal environment permits a more sensitive measurement of the achievable accuracy of side-chain prediction programs, when validating against structures obtained by X-ray crystallography. Our side-chain prediction program uses an all-atom force field and a Generalized Born model of solvation and is thus capable of modeling simple packing effects (i.e. van der Waals interactions), electrostatic effects, and desolvation, which are all important mechanisms by which the crystal environment impacts observed side-chain conformations. Our results are also relevant to the understanding of changes in side-chain conformation that may result from ligand docking and protein-protein association, insofar as the results reveal how side-chain conformations change in response to their local environment.

Computer Simulation↗
PubMed2002

Theoretical study on the stability of N-glycosyl bonds: why does N7-platination not promote depurination?

The depurination reaction of guanosine, protonated or modified with cisplatin at the N7 position, has been studied by density functional theory (DFT), coupled with a continuum treatment of solvation. Protonation accelerates the depurination reaction whereas N7-platination, the initial product of cisplatin binding to DNA, does not. The computed reaction energy profiles demonstrate that N7-platination has only a minor effect on the energetics of the transition state, whereas protonation lowers it by approximately 10 kcal mol(-1). The orbitals involved in N7-Pt/H bonding are examined, and electronic differences between the two substituted guanines are identified. Natural bond orbital analysis, fragment orbital analysis, and extended transition-state theory reveal how the electronically different substituents at the N7 position control the stability of the N9-C1' bond. The detailed description of the electronic structure of the N7-substituted guanosines and the computational protocol developed to obtain a realistic model for these systems not only explain a longstanding enigma but also provide guidelines for further studies toward understanding the interactions of cisplatin with DNA.

Cisplatin↗
PubMed2002

Dynamics of alkane hydroxylation at the non-heme diiron center in methane monooxygenase.

Semiclassical molecular dynamics simulations have been combined with quantum chemistry calculations to provide detailed modeling of the methane and ethane hydroxylation reactions catalyzed by the hydroxylase enzymes of the soluble methane monooxygenase system. The experimental distribution of enantiomeric alcohols in the reaction of ethanes made chiral by the use of hydrogen isotopes is quantitatively reproduced and explained. The reaction dynamics involve a mixture of concerted and bound radical trajectories, and we characterize each of these reactive channels in detail. Diffusion of the bound radical intermediate at the active site core determines the global rate constant. The results also provide a qualitative rationale for the lack of ring-opened products derived from certain radical clock substrate probes and for the relative rate constants and kinetic isotope effects exhibited by a variety of substrates.

Binding Sites↗
PubMed2002

Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests.

We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model.

Algorithms↗
PubMed2002

Quantum chemical studies of methane monooxygenase: comparision with P450.

The catalytic pathways of soluble methane monooxygenase (sMMO) and cytochrome P450CAM, iron-containing enzymes, are described and compared. Recent extensive density functional ab initio electronic structure calculations have revealed many similarities in a number of the key catalytic steps, as well as some important differences. A particularly interesting and significant contrast is the role played by the protein in each system. For sMMO, the protein stabilizes various species in the catalytic cycle through a series of carboxylate shifts. This process is adequately described by a relatively compact model of the active site ( approximately 100 atoms), providing a reasonable description of the energetics of hydrogen atom abstraction. For P450CAM, in contrast, the inclusion of the full protein is necessary for an accurate description of the hydrogen atom abstraction.

Binding Sites↗
PubMed2002

Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction.

Residual dipolar couplings provide significant structural information for proteins in the solution state, which makes them attractive for the rapid determination of protein structures. While dipolar couplings contain inherent structural ambiguities, these can be reduced via an overlap similarity measure that insists that protein fragments assigned to overlapping regions of the sequence must have self-consistent structures. This allows us to determine a backbone fold (including the correct Calpha-Cbeta bond orientations) using only residual dipolar coupling data from one ordering medium. The resulting backbone structures are of sufficient quality to allow for modeling of sidechain rotamer states using a rotamer prediction algorithm and a force field employing the Surface Generalized Born continuum solvation model. We demonstrate the applicability of the method using experimental data for ubiquitin. These results illustrate the synergies that are possible between protein structural database and molecular modeling methods and NMR spectroscopy, and we expect that the further development of these methods will lead to the extraction of high resolution structural information from minimal NMR data.

Computer Simulation↗