Convergence in the QM-only and QM/MM modeling of enzymatic reactions: A case study for acetylene hydratase

We report systematic quantum mechanics-only (QM-only) and QM/molecular mechanics (MM) calculations on an enzyme-catalyzed reaction to assess the convergence behavior of QM-only and QM/MM energies with respect to the size of the chosen QM region. The QM and MM parts are described by density functional theory (typically B3LYP/def2-SVP) and the CHARMM force field, respectively. Extending our previous work on acetylene hydratase with QM regions up to 157 atoms (Liao and Thiel, J. Chem. Theory Comput. 2012, 8, 3793), we performed QM/MM geometry optimizations with a QM region M4 composed of 408 atoms, as well as further QM/MM single-point calculations with even larger QM regions up to 657 atoms. A charge deletion analysis was conducted for the previously used QM/MM model (M3a, with a QM region of 157 atoms) to identify all MM residues with strong electrostatic contributions to the reaction energetics (typically more than 2 kcal/mol), which were then included in M4. QM/MM calculations with this large QM region M4 lead to the same overall mechanism as the previous QM/MM calculations with M3a, but there are some variations in the relative energies of the stationary points, with a mean absolute deviation (MAD) of 2.7 kcal/mol. The energies of the two relevant transition states are close to each other at all levels applied (typically within 2 kcal/mol), with the first (second) one being rate-limiting in the QM/MM calculations with M3a (M4). QM-only gas-phase calculations give a very similar energy profile for QM region M4 (MAD of 1.7 kcal/mol), contrary to the situation for M3a where we had previously found significant discrepancies between the QM-only and QM/MM results (MAD of 7.9 kcal/mol). Extension of the QM region beyond M4 up to M7 (657 atoms) leads to only rather small variations in the relative energies from single-point QM-only and QM/MM calculations (MAD typically about 1–2 kcal/mol). In the case of acetylene hydratase, a model with 408 QM atoms thus seems sufficient to achieve convergence in the computed relative energies to within 1–2 kcal/mol

On the Effect of Varying Constraints in the Quantum Mechanics Only Modeling of Enzymatic Reactions: The Case of Acetylene Hydratase

Quantum mechanics only (QM-only) studies of enzymatic reactions employ a coordinate-locking scheme, in which certain key atoms at the periphery of the chosen cluster model are fixed to their crystal structure positions. We report a case study on acetylene hydratase to assess the uncertainties introduced by this scheme. Random displacements of 0.1, 0.15, and 0.2 Å were applied at the ten terminal atoms fixed in the chosen 116-atom cluster model to generate sets of ten distorted structures for each given displacement. The relevant stationary points were reoptimized under these modified constraints to determine the variations of the computed energies and geometries induced by the displacements of the fixed atoms. Displacements of 0.1 Å cause a relatively minor perturbation that can be accommodated during geometry optimization, resulting in rather small changes in key bond distances and relative energies (typically of the order of 0.01 Å and 1 kcal/mol), whereas displacements of 0.2 Å lead to larger fluctuations (typically twice as high) and may sometimes even cause convergence to different local minima during geometry optimization. A literature survey indicates that protein crystal structures with a resolution higher than 2.0 Å are normally associated with a coordinate error of less than 0.1 Å for the backbone atoms. Judging from the present results for acetylene hydratase, such uncertainties seem tolerable in the design of QM-only models with more than 100 atoms, which are flexible enough to adapt during geometry optimization and thus keep the associate uncertainties in the computed energies and bond distances at tolerable levels (around 1 kcal/mol and 0.01 Å, respectively). On the other hand, crystal structures with significantly lower resolution should be used with great caution when setting up QM-only models because the resulting uncertainties in the computational results may become larger than acceptable. The present conclusions are mostly based on systematic DFT(B3LYP) calculations with a medium-size basis set. Test calculations on selected structures confirm that similar results are obtained for larger basis sets, different functionals (ωB97X, BMK, M06), and upon including solvation and zero-point corrections, even though the fluctuations in the computed relative energies become somewhat larger in some cases

The Electronic Nature of the 1,4-β-Glycosidic Bond and Its Chemical Environment: DFT Insights into Cellulose Chemistry

The molecular understanding of the chemistry of 1,4-β-glucans is essential for designing new approaches to the conversion of cellulose into platform chemicals and biofuels. In this endeavor, much attention has been paid to the role of hydrogen bonding occurring in the cellulose structure. So far, however, there has been little discussion about the implications of the electronic nature of the 1,4-β-glycosidic bond and its chemical environment for the activation of 1,4-β-glucans toward acid-catalyzed hydrolysis. This report sheds light on these central issues and addresses their influence on the acid hydrolysis of cellobiose and, by analogy, cellulose. The electronic structure of cellobiose was explored by DFT at the BB1 K/6-31++G(d,p) level. Natural bond orbital (NBO) analysis was performed to grasp the key bonding concepts. Conformations, protonation sites, and hydrolysis mechanisms were examined. The results for cellobiose indicate that cellulose is protected against hydrolysis not only by its supramolecular structure, as currently accepted, but also by its electronic structure, in which the anomeric effect plays a key role

Accuracy of computerized tomography in determining hepatic tumor size in patients receiving liver transplantation or resection

Computerized tomography (CT) of liver is used in oncologic practice for staging tumors, evaluating response to treatment, and screening patients for hepatic resection. Because of the impact of CT liver scan on major treatment decisions, it is important to assess its accuracy. Patients undergoing liver transplantation or resection provide a unique opportunity to test the accuracy of hepatic-imaging techniques by comparison of finding of preoperative CT scan with those at gross pathologic examination of resected specimens. Forty-one patients who had partial hepatic resection (34 patients) or liver transplantation (eight patients) for malignant (30 patients) or benign (11 patients) tumors were evaluable. Eight (47%) of 17 patients with primary malignant liver tumors, four (31%) of 13 patients with metastatic liver tumors, and two (20%) of 10 patients with benign liver tumors had tumor nodules in resected specimens that were not apparent on preoperative CT studies. These nodules varied in size from 0.1 to 1.6 cm. While 11 of 14 of these nodules were 1.0 cm. These results suggest that conventional CT alone may be insufficient to accurately determine the presence or absence of liver metastases, extent of liver involvement, or response of hepatic metastases to treatment

Liver Transplantation in Older Patients

To the Editor: The impact of liver transplantation on public health policy has not been delineated, partly because of uncertainty about the upper age limit for candidacy. We have compared the outlook in 363 adult recipients of livers who were less than 50 years old (mean +SD, 35.8+8.5) and 92 recipients who were 50 to 77 years old (mean +SD, 55.7+4.8). Cyclosporine and steroids1,2 were used for immunosuppression, and monoclonal antilymphocyte globulin3 and azathioprine were added as needed. The techniques of liver transplantation4 were not influenced by the age of the patient. The indications for transplantation are shown in Figure 1…., No extract is available for articles shorter than 400 words. © 1987, Massachusetts Medical Society. All rights reserved

Deformed two center shell model

A highly specialized two-center shell model has been developed accounting for the splitting of a deformed parent nucleus into two ellipsoidaly deformed fragments. The potential is based on deformed oscillator wells in direct correspondance with the shape change of the nuclear system. For the first time a potential responsible for the necking part between the fragments is introduced on potential theory basis. As a direct consequence, spin-orbit {\bf ls} and {\bf l$^2$} operators are calculated as shape dependent. Level scheme evolution along the fission path for pairs of ellipsoidaly deformed fragments is calculated. The Strutinsky method yields the shell corrections for different mass asymmetries from the superheavy nucleus $^{306}$122 and $^{252}$Cf all along the splitting process.Comment: 32 pages, 8 figure

Additive-enhanced coarsening and smoothening of metal films: Complex mass-flow dynamics underlying nanostructure evolution

Exposure of Ag/Ag(100) thin films to molecular oxygen (O2) at 220–250 K is shown to activate low-temperature coarsening of submonolayer island distributions, and a smoothing of multilayer films with “mounded” morphologies. Dissociation of O2 at kink sites populates step edges with atomic oxygen (O), modifying the step-edge energetics, and facilitating Ostwald ripening of film nanostructures. We propose that ripening occurs by “easy” detachment and terrace diffusion of an AgnO species. Cluster diffusion does not play a significant role, contrasting with the O-free system

Determinants of Regioselectivity and Chemoselectivity in Fosfomycin Resistance Protein FosA from QM/MM Calculations

FosA is a manganese-dependent enzyme that utilizes a Mn2+ ion to catalyze the inactivation of the fosfomycin antibiotic by glutathione (GSH) addition. We report a theoretical study on the catalytic mechanism and the factors governing the regioselectivity and chemoselectivity of FosA. Density functional theory (DFT) calculations on the uncatalyzed reaction give high barriers and almost no regioselectivity even when adding two water molecules to assist the proton transfer. According to quantum mechanics/molecular mechanics (QM/MM) calculations on the full solvated protein, the enzyme-catalyzed glutathione addition reaction involves two major chemical steps that both proceed in the sextet state: proton transfer from the GSH thiol group to the Tyr39 anion and nucleophilic attack by the GSH thiolate leading to epoxide ring-opening. The second step is rate-limiting and is facilitated by the presence of the high-spin Mn2+ ion that functions as a Lewis acid and stabilizes the leaving oxyanion through direct coordination. The barrier for C1 attack is computed to be 8.9 kcal/mol lower than that for C2 attack, in agreement with the experimentally observed regioselectivity of the enzyme. Further QM/MM calculations on the alternative water attack predict a concerted mechanism for this reaction, where the deprotonation of water, nucleophilic attack, and epoxide ring-opening take place via the same transition state. The calculated barrier is 8.3 kcal/mol higher than that for GSH attack, in line with the observed chemoselectivity of the enzyme, which manages to catalyze the addition of GSH in the presence of water molecules around its active site. The catalytic efficiency, regioselectivity, and chemoselectivity of FosA are rationalized in terms of the influence of the active-site protein environment and the different stabilization of the distorted substrates in the relevant transition states