How Does Acetylcholine Lose Trimethylamine? A Density Functional Theory Study of Four Competing Mechanisms

Low-energy collision-induced dissociation (CID) of acetylcholine (ACh) yields only two fragment ions: the dominant C(4)H(7)O(2)(+) ion at m/z 87, arising from trimethylamine loss; and protonated trimethylamine at m/z 60. Since the literature is replete with conflicting mechanisms for the loss of trimethylamine from ACh, in this article density functional theory (DFT) calculations are used to assess four competing mechanisms: (1) Path A involves a neighboring group attack to form a five-membered ring product, 2-methyl-1,3-dioxolan-2-ylium cation; (2) Path B is a neighboring group attack to form a three-membered ring product, 1-methyl-oxiranium ion; (3) Path C involves an intramolecular elimination reaction to form CO protonated vinylacetate; and (4) Path D is a 1,2-hydride migration reaction forming CH(2)-protonated vinylacetate. At the MP2/6-311++G(2d,p)//B3-LYP/6-31+G(d,p) level of theory path A is the kinetically favored pathway, with a transition-state energy barrier of 37.7 kcal mol(-1) relative to the most stable conformer of ACh. The lowest energy pathway for the formation of protonated trimethylamine was also calculated to proceed via path A, involving proton transfer within the ion-molecule complex intermediate, with the exocylic methyl group being the proton donor. To confirm the site of proton transfer, low-energy CID of acetyl-d(3)-choline (d(3)-ACh) was carried out, which revealed loss of trimethylamine and the formation of Me(3)ND(+).     

How Does the Axial Ligand of Cytochrome P450 Biomimetics Influence the Regioselectivity of Aliphatic versus Aromatic Hydroxylation?

How deep is your orbital? Density functional theory studies on the axial ligand effect of aliphatic versus aromatic hydroxylation of ethylbenzene by iron–oxo complexes with a variable axial ligand show that strong (anionic) ligands pull the metal inside the plane of the haeme and destabilise cationic intermediates through orbital interactions (see picture).

     

How Do Metal Ions Modulate the Rate-Determining Electron-Transfer Step in Cytochrome P450 Reactions?

Cytochrome P450 (CYP450) enzymes play important roles in maintaining human health and their reaction rates are dependent on the first electron transfer from the reduction partner. Interestingly, experimental work has shown that this step is highly influenced by the addition of metal ions. To understand the effect of external perturbations on the CYP450 first reduction step, we have performed a computational study with model complexes in the presence of metal and organic ions, solvent molecules, and an electric field. The results show that these medium-range interactions affect the driving force as well as electron-transfer rates dramatically. Based on the location, distance, and direction of the ions/electric field, the catalytic reaction rates are enhanced or impaired. Calculations on a large crystal structure with bonded alkali metal ions indicated inhibition patterns of the ions. Therefore, we predict that the active forms of the natural CYP450 isozymes will not have more than one alkali metal ion bound in the second-coordination sphere. As such, this study provides an insight into the activity of CYP450 enzymes and the effects of ions and electric field perturbations on their activity.     

Lignin Biodegradation by a Cytochrome P450 Enzyme: A Computational Study into Syringol Activation by GcoA

A recently characterized cytochrome P450 isozyme GcoA activates lignin components through a selective O-demethylation or alternatively an acetal formation reaction. These are important reactions in biotechnology and, because lignin is readily available; it being the main component in plant cell walls. In this work we present a density functional theory study on a large active site model of GcoA to investigate syringol activation by an iron(IV)-oxo heme cation radical oxidant (Compound I) leading to hemiacetal and acetal products. Several substrate-binding positions were tested and full energy landscapes calculated. The study shows that substrate positioning determines the product distributions. Thus, with the phenol group pointing away from the heme, an O-demethylation is predicted, whereas an initial hydrogen-atom abstraction of the weak phenolic O-H group would trigger a pathway leading to ring-closure to form acetal products. Predictions on how to engineer P450 GcoA to get more selective product distributions are given.     

How do azoles inhibit cytochrome P450 enzymes? A density functional study

To examine how azole inhibitors interact with the heme active site of the cytochrome P450 enzymes, we have performed a series of density functional theory studies on azole binding. These are the first density functional studies on azole interactions with a heme center and give fundamental insight into how azoles inhibit the catalytic function of P450 enzymes. Since azoles come in many varieties, we tested three typical azole motifs representing a broad range of azole and azole-type inhibitors: methylimidazolate, methyltriazolate, and pyridine. These structural motifs represent typical azoles, such as econazole, fluconazole, and metyrapone. The calculations show that azole binding is a stepwise mechanism whereby first the water molecule from the resting state of P450 is released from the sixth binding site of the heme to create a pentacoordinated active site followed by coordination of the azole nitrogen to the heme iron. This process leads to the breaking of a hydrogen bond between the resting state water molecule and the approaching inhibitor molecule. Although, formally, the water molecule is released in the first step of the reaction mechanism and a pentacoordinated heme is created, this does not lead to an observed spin state crossing. Thus, we show that release of a water molecule from the resting state of P450 enzymes to create a pentacoordinated heme will lead to a doublet to quartet spin state crossing at an Fe-OH(2) distance of approximately 3.0 A, while the azole substitution process takes place at shorter distances. Azoles bind heme with significantly stronger binding energies than a water molecule, so that these inhibitors block the catalytic cycle of the enzyme and prevent oxygen binding and the catalysis of substrate oxidation. Perturbations within the active site (e.g., a polarized environment) have little effect on the relative energies of azole binding. Studies with an extra hydrogen-bonded ethanol molecule in the model, mimicking the active site of the CYP121 P450, show that the resting state and azole binding structures are close in energy, which may lead to chemical equilibrium between the two structures, as indeed observed with recent protein structural studies that have demonstrated two distinct azole binding mechanisms to P450 heme.     

Catalytic Mechanism of Cytochrome P450 2D6 for 4-Hydroxylation of Aripiprazole： A QM/MM Study

Drug metabolism is an important issue in drug discovery. Understanding how a drug is metabolized in the body will provide helpful information for lead optimization. Cytochrome P450 2D6 （CYP2D6） is a key enzyme for drug metabolism and responsible for the metabolism of about one third marketed drugs. Aripiprazole is an atypical an- tipsychotic and metabolized by CYP2D6 to its hydroxylated form. In this study, a series of computational methods were performed to understand how CYP2D6 accomplishes the 4-hydroxylation of aripiprazole. Molecular docking and molecular dynamics simulations were first performed to prepare the initial conformations for QM/MM calcula- tions. The results revealed two possible conformations for the drug-CYP2D6 complex. The ONIOM method for QM/MM calculations was then carried out to show detailed reaction pathways for the CYP2D6-catalyzed aripipra- zole hydroxylation reaction, which demonstrated that the dominant reactive channel was electrophilic and involved an initial attack on the n-system of the dichlorophenyl group of aripiprazole to produce cation δ-complex. Further- more, the product complex for each conformation was thermodynamically stable, which is in good agreement with previous reports.     

Do Flavonoids from Durum Wheat Contribute to Its Bioactive Properties? A Prospective Study

A clear gap with respect to the potential biological properties of wheat flavonoids exists in the available literature. This information is crucial for breeding programs aiming to produce new varieties presenting improved health benefits. Accordingly, advanced breeding lines of whole durum wheat were evaluated in this contribution. The highest recovery of phenolics was achieved using aqueous acetone (50:50, v/v), as verified by multi-response optimization, thus showing that phenolics could be largely underestimated by employing an inappropriate extraction. The concentration of derivatives of apigenin, the main phenolics present, ranged from 63.5 to 80.7%, as evaluated by LC–ESI-QTOF-MS. Phenolics from the breeding line 98 exhibited the highest ability in scavenging peroxyl radicals, reducing power as well as in terms of inhibition of pancreatic lipase activity, a key enzyme regulating the absorption of triacylglycerols. In contrast, none of the samples exhibited a significant anti-diabetic potential. Despite their high concentration compared to that of phenolic acids, results of this work do not support a significant antioxidant and pancreatic lipase inhibitory effect of durum wheat flavonoids. Therefore, breeding programs and animal and/or human trials related to the effect of durum wheat flavonoids on oxidative stress and absorption of triacylglycerols are discouraged at this point.     

Drug Metabolism by Cytochrome P450 Enzymes: What Distinguishes the Pathways Leading to Substrate Hydroxylation Over Desaturation?

Cytochrome P450 enzymes are highly versatile biological catalysts in our body that react with a broad range of substrates. Key functions in the liver include the metabolism of drugs and xenobiotics. One particular metabolic pathway that is poorly understood relates to the P450 activation of aliphatic groups leading to either hydroxylation or desaturation pathways. A DFT and QM/MM study has been carried out on the factors that determine the regioselectivity of aliphatic hydroxylation over desaturation of compounds by P450 isozymes. The calculations establish multistate reactivity patterns, whereby the product distributions differ on each of the spin‐state surfaces; hence spin‐selective product formation was found. The electronic and thermochemical factors that determine the bifurcation pathways were analysed and a model that predicts the regioselectivity of aliphatic hydroxylation over desaturation pathways was established from valence bond and molecular orbital theories. Thus, the difference in energy of the O?H versus the O?C bond formed and the π‐conjugation energy determines the degree of desaturation products. In addition, environmental effects of the substrate binding pocket that affect the regioselectivities were identified. These studies imply that bioengineering P450 isozymes for desaturation reactions will have to include modifications in the substrate binding pocket to restrict the hydroxylation rebound reaction.     

ChemInform Abstract: Where Do the Forces in Molecules Come from? A Density Functional Study of N2 and HCl.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.     

Origin of the Regioselective Fatty‐Acid Hydroxylation versus Decarboxylation by a Cytochrome P450 Peroxygenase: What Drives the Reaction to Biofuel Production?

The cytochromes P450 are heme‐based mono‐oxygenases or peroxygenases involved in vital reaction processes for human health. A recently described P450 per‐oxygenase, OleT_JE, converts long‐chain fatty acids to terminal olefins and as such may have biotechnological relevance in biodiesel production. However, the reaction produces significant amounts of α‐ and β‐hydroxylation by‐products, and their origin are poorly understood. Herein, we elucidate through a QM/MM study on the bifurcation pathways how the three possible products are generated and show how the enzyme can be further engineered for optimum desaturase activity. The studies showed that the polarity and the solvent accessibility of the substrate in the binding pocket destabilize the OH‐rebound pathways and kinetically enable a thermodynamically otherwise unfavorable decarboxylation reaction. The origins of the bifurcation pathways are analyzed with valence‐bond models that highlight the differences in reaction mechanism.     

How Is a Metabolic Intermediate Formed in the Mechanism‐Based Inactivation of Cytochrome P450 by Using 1,1‐Dimethylhydrazine: Hydrogen Abstraction or Nitrogen Oxidation?

A precise understanding of the mechanism‐based inactivation of cytochrome P450 enzymes (P450s) at the quantum mechanical level should allow more reliable predictions of drug–drug interactions than those currently available. Hydrazines are among the molecules that act as mechanism‐based inactivators to terminate the function of P450s, which are essential heme enzymes responsible for drug metabolism in the human body. Despite its importance, the mechanism explaining how a metabolic intermediate (MI) is formed from hydrazine is not fully understood. We used density functional theory (DFT) calculations to compare four possible mechanisms underlying the reaction between 1,1‐dimethylhydrazine (or unsymmetrical dimethylhydrazine, UDMH) and the reactive compound I (Cpd I) intermediate of P450. Our DFT calculations provided a clear view on how an aminonitrene‐type MI is formed from UDMH. In the most favorable pathway, hydrogen is spontaneously abstracted from the N2 atom of UDMH by Cpd I, followed by a second hydrogen abstraction from the N2 atom by Cpd II. Nitrogen oxidation of nitrogen atoms and hydrogen abstraction from the C? H bond of the methyl group were found to be less favorable than the hydrogen abstraction from the N? H bond. We also found that the reaction of protonated UDMH with Cpd I is rather sluggish. The aminonitrene‐type MI binds to the ferric heme more strongly than a water molecule. This is consistent with the notion that the catalytic cycle of P450 is impeded when such an MI is produced through the P450‐catalyzed reaction.     

Constrained Density Functional Theory Plus the Hubbard U Correction Approach for the Electronic Polaron Mobility: A Case Study of TiO2?

The formation and migration of polarons have important influences on physical and chemical properties of transition metal oxides. Density functional theory plus the Hubbard \begin{document}$U$\end{document} correction (DFT+\begin{document}$U$\end{document}) and constrained density functional theory (cDFT) are often used to obtain the transfer properties for small polarons. In this work we have implemented the cDFT plus the Hubbard \begin{document}$U$\end{document} correction method in the projector augmented wave (PAW) framework, and applied it to study polaron transfer in the bulk phases of TiO\begin{document}$_2$\end{document}. We have confirmed that the parameter \begin{document}$U$\end{document} can have significant impact on theoretical prediction of polaronic properties. It was found that using the Hubbard \begin{document}$U$\end{document} calculated by the cDFT method with the same orbital projection as used in DFT+\begin{document}$U$\end{document}, one can obtain theoretical prediction of polaronic properties of rutile and anatase phases of TiO\begin{document}$_2$\end{document} in good agreement with experiment. This work indicates that the cDFT+\begin{document}$U$\end{document} method with consistently evaluated \begin{document}$U$\end{document} is a promising first-principles approach to polaronic properties of transition metal oxides without empirical input.     

How and Why Does Ni0 Promote Smooth Etheric CO Bond Cleavage and CC Bond Formation? A Theoretical Study

Ni‐catalyzed cross‐coupling between aryl alkyl ethers (ArOR) and Grignard reagents (RMgBr), known since 1979, proceeds under mild conditions in many cases. Although the reaction routes of various synthetic protocols involving transition‐metal‐catalyzed C?O bond activation have been elucidated, the mechanism of this etheric Kumada–Tamao–Curriu reaction remains enigmatic. This is because oxidative addition of inert etheric C?O to Ni⁰ is thermodynamically and kinetically unfavorable, making it hard to explain the observed high reactivity of ether toward Ni catalysts. In this work, we used DFT calculations to identify a plausible reaction pathway by the Ni⁰‐ate complex, which enables smooth C?O bond cleavage and R‐group transfer with reasonable activation barriers; this mechanism also accounts for the ineffectiveness of Pd catalysts. These results throw new light on both C?O activation and cross‐coupling, and should be valuable for further rational development of the methodologies.     

Can Anisotropic Exchange Be Reliably Calculated Using Density Functional Methods? A Case Study on Trinuclear MnIII‐MIII‐MnIII (M=Fe,Ru, and Os) Cyanometalate Single‐Molecule Magnets

Density functional studies have been performed on a set of trinuclear single‐molecule magnets (SMMs) of general formula [{Mn₂(5‐Br salen)₂(MeOH)₂}M(CN)₆](NEt₄) (M=Fe^III ( 1 ), Ru^III ( 2 ) and Os^III ( 3 ); 5‐Brsalen=N,N′‐ethylenebis(5‐bromosalicylidene)iminato anion). We have computed the orbital‐dependent exchange interaction for all three complexes for the first time using DFT and complete active space self‐consistent field (CASSCF) methods. DFT calculations yield the anisotropic exchange as J_ξξ=3.5 cm^?1 for 1 ; J_ξξ=12.1 cm^?1, J_ζζ=?6.9 cm^?1 and J_ηη=?14 cm^?1 for 2 ; and J_ξξ=23.7 cm^?1 and J_ζζ=?11.1 cm^?1 for 3 . The computed values are in agreement with the experimental report, and this suggests that the established methodology can be used to compute the anisotropic exchange in larger clusters. Our calculations reiterate the fact that the exchange is described by a three‐axis anisotropic exchange for complexes 2 and 3 as evidenced by the experiments. A stronger exchange coupling as we move down the periodic table from 3d to 5d is reproduced by our calculations, and the origin of this enhancement in the exchange interaction has been probed by using molecular orbital analysis. The electronic origin of different types of exchange observed in this series is found to be related to the energy difference between possible degenerate pairs and the nature of orbital interactions. By computing the exchange interaction, the single‐ion anisotropy of Mn^III and zero‐field splitting of the S=9/2 ground state of complexes 1 – 3 using CASSCF and/or DFT methods, we have attempted to shed light on the issue of anisotropic exchange and the barrier height for the magnetisation reversal in SMMs. Comprehensive magneto–structural correlations have been developed to offer clues on how to further enhance the barrier height in this class of SMMs.     

Discrimination of σ‐Bond Metathesis Pathways in H/D Exchange Reactions on [(SiO)3Zr?H]: A Density Functional Theory Study

The mechanism of the H/D exchange reaction in alkane/hydrogen mixtures on silica‐supported zirconium hydride was investigated by a modelling study using density functional theory (DFT) calculations. The electronic activation enthalpy (ΔH ) for the C? H bond activation step (TS₃) was calculated to be around 92 kJ mol^?1, whereas it would be 258 kJ mol^?1 for a direct exchange process (TS₁, also called the kite TS). These data clearly speak in favour of the former as a mechanism for C? H bond scrambling. Moreover, the calculated enthalpy of activation (ΔH ) for H/D exchange in H₂/D₂ mixtures (TS₂) is 33.5 kJ mol^?1, which shows that this reaction is much faster than the H/D scrambling in alkane/H₂ mixtures, as shown experimentally. Additionally, the calculated activation entropies (For TS_1–4, ΔS ranges between ?129 and ?174 J mol^?1 K^?1) are very negative. Although the calculated activation entropies are also in full agreement with experimental data (ΔS =?113 J mol^?1 K^?1), overall, the calculated activation enthalpies are much higher than the experimental ones. This suggests that the actual catalyst is probably more electrophilic than the model chosen for the calculations.     

Is an M?N σ‐Bond Insertion Route a Viable Alternative to the MN [2+2] Cycloaddition Route in Intramolecular Aminoallene Hydroamination/Cyclisation Catalysed by Neutral Zirconium Bis(amido) Complexes? A Computational Mechanistic Study

This study examines alternative reaction channels for intramolecular hydroamination/cyclisation (IHC) of primary 4,5-hexadien-1-ylamine aminoallene (1) by a neutral [Cp(2)ZrMe(2)] zirconocene precatalyst (2) by using the density functional theory (DFT) method. The first channel proceeds through a [Cp(2)Zr(NHR)(2)] complex as the reactive species and relevant steps including the insertion of an allenic C=C linkage into the Zr--NHR sigma-bond and ensuing protonolysis. This is contrasted to the [2+2] cycloaddition mechanism involving a [Cp(2)Zr=NR] transient species. The salient features of the rival mechanisms are disclosed. The cycloaddition route entails the first transformation of the dormant [Cp(2)Zr(NHR)(2)] complex 3 B into the transient [Cp(2)Zr=NR] intermediate 3 A', which is turnover limiting. This route features a highly facile ring closure together with a substantially slower protonolysis (k(cycloadd)>k(protonolysis)) and can display inhibition by high substrate concentration. In contrast, protonolysis is the more facile step for the channel proceeding through the [Cp(2)Zr(NHR)(2)] complex as the catalytically active species. Here, C=C insertion into the Zr--C sigma-bond of 3 B, which represents the catalyst resting state, is turnover limiting and substrate concentration is unlikely to influence the rate. The regulation of the selectivity is elucidated for the two channels. DFT predicts that five-ring allylamine and six-ring imine are generated upon traversing the cycloaddition route, thereby comparing favourably with experiment, whereas the cycloimine should be formed solely along the sigma-bond insertion route. The mechanistic analysis is indicative of an operating [2+2] cycloaddition mechanism. The Zr--NHR sigma-bond insertion route, although appearing not to be employed for the reactants studied herein, is clearly suggested as being viable for hydroamination by charge neutral organozirconium compounds.