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The detection of phosphorous-bearing molecules in interstellar environments constitutes a fundamental task for understanding the formation of prebiotic molecules, but it is also a challenge. In cold interstellar environments, where rich chemistry is expected to happen, only PN and PO have been detected. Phosphine (PH3) must also play an essential role in these regions, since P is expected to deplete onto dust grains significantly, and hydrogenation reactions are dominant in such environments. Surface chemistry on dust grains shows a particular idiosyncrasy where an equilibrium between competitive reactions, photoconversion processes, and desorption are in continuous interplay, modifying both the dust composition and the gas composition. In this study, we theoretically study in detail the interconversion of P to PH3 via subsequent additions of H on cold dust grain analogs. For all reactions, we provide the binding energy of the adsorbates, reaction energies, and, when present, activation barriers and tunneling-corrected rate constants. We also present an estimate of the desorption temperature of these species based on transition state theory. Using recently available experimental results on PH3 desorption via chemical reactions, we conclude that all of the intermediate products of the hydrogenation sequence to phosphine may be released to the gas phase. [ABSTRACT FROM AUTHOR]

Umbrella integration is a method to analyze umbrella sampling simulations by calculating and integrating the mean force. Here, the method is extended to multidimensional reaction coordinates. Approximation of the probability distribution obtained from sampling by a multivariate normal distribution allows to calculate the mean force from the average and the covariance matrix of the reaction coordinate. Integration schemes of the free-energy gradient field are discussed. Integration on a real-space grid is compared to expansion of the gradient in a series of analytic functions (such as a Fourier analysis), which can be integrated, and the expansion of the gradient only at the window means in a series of analytic functions. The Fourier analysis was found particularly useful for periodic reaction coordinates, such as torsion angles. An expression is provided to calculate the Hessian of the free energy with respect to the reaction coordinates from sampling data. The utility of the method is demonstrated at the example of the free-energy surface of the alanine dipeptide in vacuum calculated with respect to the backbone torsion angles [uppercase_phi_synonym] and Ψ. Relevance of the Jacobian term for non-Cartesian reaction coordinates is discussed. [ABSTRACT FROM AUTHOR]

Umbrella sampling simulations, or biased molecular dynamics, can be used to calculate the free-energy change of a chemical reaction. We investigate the sources of different sampling errors and derive approximate expressions for the statistical errors when using harmonic restraints and umbrella integration analysis. This leads to generally applicable rules for the choice of the bias potential and the sampling parameters. Numerical results for simulations on an analytical model potential are presented for validation. While the derivations are based on umbrella integration analysis, the final error estimate is evaluated from the raw simulation data, and it may therefore be generally applicable as indicated by tests using the weighted histogram analysis method. [ABSTRACT FROM AUTHOR]

The protonation of N2 bound to the active center of nitrogenase has been investigated using state-of-the-art density-functional theory calculations. Dinitrogen in the bridging mode is activated by forming two bonds to Fe sites, which results in a reduction of the energy for the first hydrogen transfer by 123 kJ/mol. The axial binding mode with open sulfur bridge is less reactive by 30 kJ/mol and the energetic ordering of the axial and bridged binding modes is reversed in favor of the bridging dinitrogen during the first protonation. Protonation of the central ligand is thermodynamically favorable but kinetically hindered. If the central ligand is protonated, the proton is transferred to dinitrogen following the second protonation. Protonation of dinitrogen at the Mo site does not lead to low-energy intermediates. [ABSTRACT FROM AUTHOR]

A detailed analysis of the C(sp3)−H activation process by vinylidene AuI complexes is described based on an intrinsic bond orbital analysis. Based on our analysis this event can be divided into three phases: (i) hydride transfer, (ii) C−C bond formation, and (iii) σ to π rearrangement of the lone pair coordinated to Au. Small perturbations of the system lead to either a concerted asynchronous reaction, or a stepwise reaction featuring an intermediate with a C-H-C three-centre two-electron (3c-2e) bond. The role of π-donating substituents is highlighted and provides a way of controlling reactions of this type in future experimental studies. [ABSTRACT FROM AUTHOR]

The potential of vinyl Au species to react either through a controlled π- or σ-pathway is demonstrated. This nomenclature is directly derived from the orbitals of the vinyl Au species leading to the newly formed bonds. When the π-bond of the vinyl Au intermediate is transformed into a σ-bond, we name it π-pathway, and a σ- to σ- transformation is named σ-pathway. Examples of reactions following these pathways are a Au-catalysed [3,3]-sigmatropic rearrangement and a protodeauration reaction. These reactions have been studied using intrinsic bond orbitals (IBOs) and allow for the clear identification of these pathways. Energies for the reaction path of the Au-catalysed [3,3]-sigmatropic rearrangement were in addition computed using CCSD(T)-F12. Analysis of the intrinsic reaction coordinate (IRC) of the [3,3]-sigmatropic rearrangement using IBOs further allows us to refine the previous mechanistic proposal and identifies a hidden intermediate along the reaction path. [ABSTRACT FROM AUTHOR]

Salicylate 1,2-dioxygenase (SDO) is the first enzyme to be discovered to catalyze the oxidative cleavage of a monohydroxylated aromatic compound, namely salicylate, instead of the well-known electron-rich substrates. We have investigated the mechanism of dioxygen activation in SDO by QM/MM calculations. Our study reveals that the non-heme FeII center in SDO activates salicylate and O2 synergistically through a strong covalent interaction to facilitate the reductive cleavage of O2. A covalent salicylate-FeII-O2 complex is the reactive oxygen species in this case, and its electronic structure is best described as being between the two limiting cases, FeII−O2 and FeII−O2.−, with partial electron transfer from the activated salicylate to O2 via the Fe center. Thus SDO employs a synergistic strategy of substrate and oxygen activation to carry out the catalytic reaction, which is unprecedented in the family of iron dioxygenases. Moreover, O2 activation in SDO happens without the assistance of a proton source. Our study essentially shows a new mechanistic possibility for O2 activation. [ABSTRACT FROM AUTHOR]

The catalytic cycle of acetylene reduction at the FeMo cofactor of nitrogenase has been investigated on the basis of density functional theory. C2H2 binds to the same site as N2, but it binds to a less reduced state of the cofactor. In a manner similar to that of N2 binding, one of the sulfur bridges opens during acetylene binding. The model explains the strong noncompetitive inhibition of N2 reduction by C2H2 and the weak competitive inhibition of C2H2 reduction by N2. Our proposed mechanism is consistent with experimentally observed stereoselectivity and the ability of C2H2 to suppress H2 production by nitrogenase. [ABSTRACT FROM AUTHOR]

The calculation of free-energy barriers by umbrella sampling and many other methods is hampered by the necessity for an a priori choice of the reaction coordinate along which to sample. We avoid this problem by providing a method to search for saddle points on the free-energy surface in many coordinates. The necessary gradients and Hessians of the free energy are obtained by multidimensional umbrella integration. We construct the minimum free-energy path by following the gradient down to minima on the free-energy surface. The change of free energy along the path is obtained by integrating out all coordinates orthogonal to the path. While we expect the method to be applicable to large systems, we test it on the alanine dipeptide in vacuum. The minima, transition states, and free-energy barriers agree well with those obtained previously with other methods. [ABSTRACT FROM AUTHOR]

Quantum mechanical tunneling of atomsplays a significant rolein many chemical reactions. The crossover temperature between classicaland quantum movement is a convenient preliminary indication of theimportance of tunneling for a particular reaction. Here we show, usinginstanton theory, that quantum tunneling is possible significantlyabove this crossover temperature for specific forms of the potentialenergy surface. We demonstrate the effect on an analytic potentialas well as a chemical system. While protons move asynchronously alonga Grotthuss chain in the classical high-temperature range, the onsetof tunneling results in a synchronization of their movement. [ABSTRACT FROM AUTHOR]

• Sulfur atom tunneling in the S 4 N 4 ring flipping reaction is impossible. • Not only the mass, but also the barrier width and height are critical for tunneling. • Beyond second row elements, the mass and/or the barrier width makes tunneling close to impossible. • Caution must be exercised when predicting experimentally observable reactions. In a recent article (Chem. Phys. Lett. 749 (2020), 137440), Kumar and Mallick predict by computations that a sulfur atom tunneling mechanism leads to a ring flipping reaction of S 4 N 4 below 70 K. Herein, on the basis of their tunneling computations, it is shown that the sulfur atom tunneling is not viable, and therefore impossible to be probed experimentally. Based on this, we discuss the prerequisites for a chemical reaction to be driven by heavy atom tunneling. [ABSTRACT FROM AUTHOR]

The anionic high oxidation state molybdenum (VI) amidato bisalkyl alkylidyne complex [(Mo(N-2,6-Me 2 -C 6 H 3 )(CH 2 CMe 3 ) 2 (CCMe 2 Ph)(Mg . Et 2 O-μ-Cl) 2 ], 1 , is reported. It forms via reaction of Mo(N-2,6-Me 2 -C 6 H 3 )(CHCMe 2 Ph)(O 3 SCF 3 ) 2 . DME (DME = 1,2-dimethoxyethane), with an excess of neopentylmagnesium chloride. DFT calculations suggest a mesomerization between an amidato-alkylidyne and imido alkylidenato complex. [ABSTRACT FROM AUTHOR]