Fragmentation of conjugated amides at the C?C(O) bond in electrospray mass spectrometry: a proton‐bound dimeric intermediate identified by the kinetic method

Fragmentation of protonated amides in mass spectrometry at the C? C(O) bond, which competes with the C(O)? N bond cleavage, was observed when the amide group is conjugated with an unsaturated moiety. In the case of N‐methylbenzamides bearing different substituents, this reaction gives rise to protonated methyl isocyanate and protonated benzenes. The kinetic method was applied to this reaction in spite of the fact that this is a fragmentation of a molecular species (rather than proton‐bound dimers). A correlation is established between the intensities of the two product ions and the proton affinities (PAs) of the corresponding fragment molecules, which is similar to that when the kinetic method is used in the determination of PAs on proton‐bound dimers. This result provides strong evidence that the reaction proceeds via a proton‐bound methyl isocyanate/benzene complex intermediate. In addition, the PA of isocyanic acid, which is involved in the fragmentation of unsubstituted benzamide, is compared with that of benzene and a downward revised value, 175 kcal/mol, is recommended. Copyright © 2004 John Wiley & Sons, Ltd.     

Deciphering the potassium storage phase conversion mechanism of phosphorus by combined solid-state NMR spectroscopy and density functional theory calculations

Phosphorus is the potential anode material for emerging potassium-ion batteries(PIBs) owing to the highest specific capacity and relatively low operation plateau. However, the reversible delivered capacities of phosphorus-based anodes, in reality, are far from the theoretical capacity corresponding to the formation of K₃P alloy. And, their underlying potassium storage mechanisms remain poorly understood.To address this issue, for the first time, we perform high-resolution solid-state ...     

Kinetic energy density for orbital‐free density functional calculations by axiomatic approach

An axiomatic approach is herein used to determine the physically acceptable forms for general D‐dimensional kinetic energy density functionals (KEDF). The resulted expansion captures most of the known forms of one‐point KEDFs. By statistically training the KEDF forms on a model problem of noninteracting kinetic energy in 1D (six terms only), the mean relative accuracy for 1000 randomly generated potentials is found to be better than the standard KEDF by several orders of magnitudes. The accuracy improves with the number of occupied states and was found to be better than for a system with four occupied states. Furthermore, we show that free fitting of the coefficients associated with known KEDFs approaches the exactly analytic values. The presented approach can open a new route to search for physically acceptable kinetic energy density functionals and provide an essential step toward more accurate large‐scale orbital free density functional theory calculations.     

Improvement of initial guess via grid‐cutting for efficient grid‐based density functional calculations

We introduced an efficient initial guess method, namely the grid‐cutting, which is specialized for grid‐based density functional theory (DFT) calculations. It produces initial density and orbitals through pre‐DFT calculations in an inner simulation box made by cutting out the outer region of a full‐size one. To assess its performance, we carried out DFT calculations for small molecules included in the G2‐1 set and two large molecules with various combinations of mixing and diagonalization conditions, relative size of the inner box, and grid spacing. For all cases, the grid‐cutting method was more efficient than conventional ones such as extended Hückel, superposition of atomic densities, and linear combination of atomic orbitals. For instance, it was about 20% faster in computational time and about 45% smaller in the number of self‐consistent‐field cycles than the superposition of atomic densities because it provided high‐quality initial density and orbitals closer to the corresponding fully converged values. In addition, it showed good performance for non‐Coulombic model systems such as harmonic oscillator.     

Reaction mechanism of palladium‐catalyzed silastannation of allenes by density functional theory

The reaction mechanism of Pd(0)‐catalyzed allenes silastannation reaction is investigated by the density functional method B3LYP. The overall reaction mechanism is examined. For the allene insertion step, the Pd Si bond is preferred over the Pd Sn bond. The electronic mechanism of the allene insertion into Pd Si bond to form σ‐vinylpalladium (terminal‐insertion) and σ‐allylpalladium (internal‐insertion) insertion products is discussed in terms of the electron donation and back‐donation. It is found that the electron back‐donation is significant for both terminal‐ and internal‐insertion. During allene insertion into Pd Si bond, internal‐insertion is preferred over terminal‐insertion. By using methylallene, the regio‐selectivity for the monosubstituted allene insertion into Pd Si and Pd Sn bond is analyzed. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

An atomic scale mechanism for the antimalarial action of chloroquine from density functional theory calculations

The X-ray crystal structures of complexes between the antimalarial drugs quinine, quinidine and halofantrine and their biological target, iron(III) ferriprotoporphyrin IX (FePPIX), have been reported in the literature (de Villiers et al. in ACS Chem Biol 7:666, 2012; J Inorg Biochem 102:1660, 2008) and show that all three drugs utilize their zwitterionic alkoxide forms to coordinate to the iron atom via Fe–O bonds. In this work, density functional theory calculations with implicit solvent corrections have been used to model the energetics of formation of these complexes. It is found that the cost of formation of the active zwitterionic form of each drug is more than offset by the energy of its binding to FePPIX, such that the overall energies for complexation of all three drugs with FePPIX are moderately favourable in water, and rather more favourable in n-octanol as solvent. The calculations have been extended to develop an analogous model for the complex between FePPIX and chloroquine, whose structure is not presently known from experiment.     

The proton‐coupled proton transfer mechanism,H2O catalysis,and hydrogen tunneling effects in the reaction of HNCH2 with HCOOH in the interstellar medium

The reaction HNCH₂ + HCOOH → H₂NCH₂COOH is supposed to be an important reaction related to the possible origin of amino acids on the early Earth. We find that it has an energy barrier of 87.37 kcal mol⁻¹ obtained with MP2/6‐311+G** in the gas phase, but it is likely enhanced to occur in the interstellar medium (ISM) through a proton‐coupled proton transfer reaction, initiated by HNCH₂ coupled with H₂⁺, H₃⁺, or H₃⁺O. H₂⁺, H₃⁺, and H₃⁺O serve as a donor of energy in the coupled reactions. H⁺, which is a key species to the coupled reactions, further, plays a catalytic role in reducing a barrier up to 14.14 kcal mol⁻¹. In the coupled reaction with H₃⁺O, H₂O, which can seize, transport, and deliver a proton from HCOOH to H₂NCH₂⁺, reduces a barrier up to 14.96 kcal mol⁻¹. A significant hydrogen‐tunneling pathway is predicted by the temperature dependences of k_H^CVT/SCT, calculated using the small curvature tunneling (SCT) approximation and canonical variational transition state theory (CVT). Hydrogen tunneling is another important mechanism to make the reaction happen in the ISM. The achieved results can be applied to discuss the origin of amino acids from the materials of the Earth itself. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Analytical gradients for subsystem density functional theory within the slater‐function‐based amsterdam density functional program

We present a new implementation of analytical gradients for subsystem density‐functional theory (sDFT) and frozen‐density embedding (FDE) into the Amsterdam Density Functional program (ADF). The underlying theory and necessary expressions for the implementation are derived and discussed in detail for various FDE and sDFT setups. The parallel implementation is numerically verified and geometry optimizations with different functional combinations (LDA/TF and PW91/PW91K) are conducted and compared to reference data. Our results confirm that sDFT‐LDA/TF yields good equilibrium distances for the systems studied here (mean absolute deviation: 0.09 Å) compared to reference wave‐function theory results. However, sDFT‐PW91/PW91k quite consistently yields smaller equilibrium distances (mean absolute deviation: 0.23 Å). The flexibility of our new implementation is demonstrated for an HCN‐trimer test system, for which several different setups are applied. © 2016 Wiley Periodicals, Inc.     

BASHD‐J‐resolved‐COSY: a new method for measuring proton‐proton spin coupling constants of multiplet signals

An effective pulse sequence for measuring H–H coupling constants, named BASHD‐J‐resolved‐COSY, has been developed. In the spin systems such as –CH_A–CH_B(CH₃)–CH_C–, a methine proton H_B splits into a multiplet owing to several vicinal couplings, resulting in attenuation of its cross‐peak intensity. Therefore, the measurements of ³J_H–H with respect to H_B are generally difficult in the E‐COSY‐type experiments. With the aim of accurate measurements of ³J_H‐H in such a spin system, we have developed a new pulse sequence, which selectively decouples the secondary methyl group. The proposed pulse sequence provides the simplified cross‐peak patterns, which are suitable for reliable measurements of ³J_H‐H in a complicated natural product. Copyright © 2012 John Wiley & Sons, Ltd.     

Hartree–Fock and density functional theory calculations for the reaction mechanism of nitric oxide reductase cytochrome P450nor from Fusarium oxysporum

A reaction mechanism of a nitric oxide reductase, cytochrome P450nor (P450nor) from Fusarium oxysporum, was clarified by using Density functional theory and Hartree–Fock calculations. In this reaction mechanism, molecular orbital (MO) analysis revealed that the NO ligand dissociates from the heme iron immediately after one-electron reduction by NADH, and MO energy analysis revealed that NADH acts as a one-electron reducer, not as a two-electron reducer, and that NADH has a pivotal role different from other one-electron reducers. The role of NADH is to act as a double one-electron donor (i.e. one-electron transfer occurring twice) and to combine with the NO⁻ molecule by charge recombination reaction. Our quantum chemical calculations indicated that all reactions occurring in the heme pocket are too fast to become rate-limiting. Therefore, the rate-limiting steps in the proposed reaction mechanism are the process of capturing NO and NADH into the heme pocket and the process of expelling a product generated in the heme pocket. Kinetics of these processes was discussed based on large-amplitude vibration, which helps capturing and expelling processes in a widely opened heme pocket of P450nor. The reaction mechanism proposed here well explains published experimental data.     

A density functional theory study on the catalytic mechanism of hydroxycinnamoyl‐CoA hydratase‐lyase

Hydroxycinnamoyl‐CoA hydratase‐lyase (HCHL), a particular member of the crotonase superfamily, catalyzes the bioconversion of feruloyl‐CoA to the important flavor and fragrance compound vanillin. In this article, the catalytic mechanism of HCHL has been studied by using hybrid density functional theory method with simplified models. The calculated results reveal that the mechanism involves the hydration of the C?C double bond of feruloyl‐CoA and thence the cleavage of C? C single bond of β‐hydroxythioester. The hydration step is a typical concerted process, whereas C? C bond cleavage follows a concerted but asynchronous mechanism. The calculated energy barrier of hydration reaction is only slightly lower than that of cleavage process, implying both of two processes are rate limiting. By using three substrate analogs, the substrate specificity of HCHL was further examined. It is found that the p‐hydroxyl group of aromatic ring is necessary for the catalytic reaction. © 2013 Wiley Periodicals, Inc.     

Phosphoric acid catalyzed enantioselective transfer hydrogenation of imines: a density functional theory study of reaction mechanism and the origins of enantioselectivity

The phosphoric acid catalyzed reaction of 1,4‐dihydropyridines with N‐arylimines has been investigated by using density functional theory. We first considered the reaction of acetophenone PMP‐imine (PMP=p‐methoxyphenyl) with the dimethyl Hantzsch ester catalyzed by diphenyl phosphate. Our study showed that, in agreement with what has previously been postulated for other reactions, diphenyl phosphate acts as a Lewis base/Brønsted acid bifunctional catalyst in this transformation, simultaneously activating both reaction partners. The calculations also showed that the hydride transfer transition states for the E and Z isomers of the iminium ion have comparable energies. This observation turned out to be crucial to the understanding of the enantioselectivity of the process. Our results indicate that when using a chiral 3,3′‐disubstituted biaryl phosphoric acid, hydride transfer to the Re face of the (Z)‐iminium is energetically more favorable and is responsible for the enantioselectivity, whereas the corresponding transition states for nucleophilic attack on the two faces of the (E)‐iminium are virtually degenerate. Moreover, model calculations predict the reversal in enantioselectivity observed in the hydrogenation of 2‐arylquinolines, which during the catalytic cycle are converted into (E)‐iminium ions that lack the flexibility of those derived from acyclic N‐arylimines. In this respect, the conformational rigidity of the dihydroquinolinium cation imposes an unfavorable binding geometry on the transition state for hydride transfer on the Re face and is therefore responsible for the high enantioselectivity.     

Structural model studies for the peroxo intermediate P and the reaction pathway from P-->Q of methane monooxygenase using broken-symmetry density functional calculations

Several structural models for the active site of the peroxo intermediate state "P" of the hydroxylase component of soluble methane monooxygenase (MMOH) have been studied, using two DFT functionals OPBE and PW91 with broken-symmetry methodology and the conductor-like screening (COSMO) solvation model. These active site models have different O2 binding modes to the diiron center, such as the mu-eta2,eta2, trans-mu-1,2 and cis-mu-1,2 conformations. The calculated properties, including optimized geometries, electronic energies, Fe net spin populations, and M?ssbauer isomer shift and quadrupole splitting values, have been reported and compared with available experimental results. The high-spin antiferromagnetically (AF) coupled Fe3+ sites are correctly predicted by both OPBE and PW91 methods for all active site models. Our data analysis and comparisons favor a cis-mu-1,2 structure (model cis-mu-1,2a shown in Figure 9) likely to represent the active site of MMOH-P. Feasible structural changes from MMOH-P to another intermediate state MMOH-Q are also proposed, where the carboxylate group of Glu243 side chain has to open up from the mono-oxygen bridging position, and the dissociations of the terminal H2O ligand from Fe1 and of the oxygen atom in the carboxylate group of Glu144 from Fe2 are also necessary for the O2 binding mode changes from cis to trans. The O-O bond is proposed to break in the trans-conformation and forms two mu-oxo bridges in MMOH-Q. The terminal H2O molecule and the Glu144 side chain then rebind with Fe1 and Fe2, respectively, in Q.     

Polarization response of water and methanol investigated by a polarizable force field and density functional theory calculations: implications for charge transfer

Electronic polarization response in hydrogen-bond clusters and liquid configurations of water and methanol has been studied by density functional theory (DFT) and by a polarizable force field based on the chemical potential equalization (CPE) principle. It has been shown that an accurate CPE parametrization based on isolated molecular properties is not completely transferable to strongly interacting hydrogen-bond clusters with discrepancies between CPE and DFT overall dipole moments as large as 15%. This is due to the lack of intermolecular charge transfer in the standard CPE implementation. A CPE scheme for evaluating the amount of transferred charge has been developed. The charge transfer parameters are determined with the aid of accurate DFT calculations using only hydrogen-bond dimer configurations. The amount of transferred charge is found to be of the order of few hundredths of electrons, as already found in recent studies on hydrogen-bond systems. The parameters of the model are then used, without further adjustment, to different hydrogen-bond clustered forms of water and methanol (oligomer and liquid configurations). In agreement with different approaches proposed in literature for studying charge transfer effects, the transferred charge in hydrogen-bond dimers is found to decrease exponentially with the hydrogen-bond distance. When allowance is made for charge transfer according to the proposed scheme, the CPE dipole moments are found to reproduce satisfactorily the DFT data.     

Mechanism for the reaction of 2-naphthol with N-methyl-N-phenyl-hydrazine suggested by the density functional theory investigations

For the first time the computed mechanisms for the novel reaction of 2-naphthol with N-methyl-N-phenylhydrazine, leading to 1-amino-2-naphthol (Tang et al., J Am Chem Soc 2008, 130, 5840), have been investigated using the density functional theory. Four distinct possible pathways were evaluated: two amination mechanisms with the attack of NH(2) group respectively at the α-position C1 and β-position C3 atoms of 2-naphthol (pathways 1 and 2) as well as two rearrangement processes with displacement of the phenolic hydroxyl group followed by the benzidine-like rearrangement at the α-position C1 and β-position C3 atoms of 2-naphthol, respectively (pathways 3 and 4). Solvent effect has been tested based on the optimized geometries of the stationary points in solution at the B3LYP/PCM/6-31+G(d,p) level of theory with an averaged dielectric constant of binary solvent. Single-point energies of the optimized structures have been calculated using three hybrid density functionals, B3LYP, MPW3LYP, and B3PW91 with the 6-311++G(3df,2p) basis set. Our computed results clearly manifest that pathway 1 (α-amination) has the highest possibility to occur, with the Gibbs free energies being lower by 6 to 20 kcal/mol compared with the other three pathways, which leads to 1-amino-2-naphthol and N-methylaniline as products. It is in excellent agreement with the experimental observation.