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The positions of grid points for representing a multidimensional potential energy surface (PES) have a non-negligible impact on its accuracy and the associated computational effort for its generation. Six different positioning schemes were studied for PESs represented by n-mode expansions as needed for the accurate calculation of anharmonic vibrational frequencies by means of vibrational configuration interaction theory. A static approach, which has successfully been used in many applications, and five adaptive schemes based on Gaussian process regression have been investigated with respect to the number of necessary grid points and the accuracy of the fundamental modes for a small set of test molecules. A comparison with a related, more sophisticated, and consistent approach by Christiansen et al. is provided. The impact of the positions of the ab initio grid points is discussed for multilevel PESs, for which the computational effort of the individual electronic structure calculations decreases for increasing orders of the n-mode expansion. As a result of that, the ultimate goal is not the maximal reduction of grid points but rather the computational cost, which is not directly related. [ABSTRACT FROM AUTHOR]

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. It calculates free-energy changes from distributions obtained from molecular dynamics. While it can be formulated on the full sampled distributions, they are generally approximated by normal distributions. This is equivalent to the truncation of a power series of the free energy with respect to the reaction coordinate after the quadratic term or by a truncation of a cumulant expansion. Here, expressions for additional terms in the power series are derived. They can be calculated from the central moments of the distributions. This extension allows to test the approximations in applications. [ABSTRACT FROM AUTHOR]

The instanton method allows to accurately calculate tunneling rates down to very low temperature. However, with lowering the temperature, the computational effort steeply increases as many more discretization points are required. This is caused in practical applications by the majority of the discretization points accumulating at a very small region in configuration space. Here, we describe a method to flexibly discretize the instanton path adapted to the temperature. Chosen appropriately, the discretization leads to a much more uniform distribution of the images (control points) along the path which reduces the number of required images by about a factor of two. Combined with a modified Newton-Raphson optimizer and successive updates of the Hessians, the proposed method provides converged reaction rates at computational costs reduced by more than an order of magnitude. We show the success of the method on analytic test potentials and on molecules with energies directly obtained from density functional theory calculations. [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]

Algorithmic improvements of the dimer method [G. Henkelman and H. Jónsson, J. Chem. Phys. 111, 7010 (1999)] are described in this paper. Using the limited memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) optimizer for the dimer translation greatly improves the convergence compared to the previously used conjugate gradient algorithm. It also saves one energy and gradient calculation per dimer iteration. Extrapolation of the gradient during repeated dimer rotations reduces the computational cost to one gradient calculation per dimer rotation. The L-BFGS algorithm also improves convergence of the rotation. Thus, three to four energy and gradient evaluations are needed per iteration at the beginning of a transition state search, while only two are required close to convergence. Moreover, we apply the dimer method in internal coordinates to reduce coupling between the degrees of freedom. Weighting the coordinates can be used to apply chemical knowledge about the system and restrict the transition state search to only part of the system while minimizing the remainder. These improvements led to an efficient method for the location of transition states without the need to calculate the Hessian. Thus, it is especially useful in large systems with expensive gradient evaluations. [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]

We present a method to analyze biased molecular-dynamics and Monte Carlo simulations, also known as umbrella sampling. In the limiting case of a strong bias, this method is equivalent to thermodynamic integration. It employs only quantities with easily controllable equilibration and greatly reduces the statistical errors compared to the standard weighted histogram analysis method. We show the success of our approach for two examples, one analytic function, and one biological system. [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]

We have investigated the free energy surface of alanine tripeptide in water. To elucidate the secondary structure of the amide chain, information on the free energy surface with explicit water at room temperature, and the multidimensional reaction coordinates are required. We studied the minimum free energy paths (MFEPs) connecting reactants, transition structures (TS) and products. To solve this problem, we used the free energy reaction root mapping (FERRMap) method. This is an automated search method to find MFEPs by using umbrella integration and the scaled hypersphere search method. We calculated the four-dimensional free energy surface for alanine tripeptide in water using FERRMap and found 61 equilibrium structures (EQ) connected by 133 TS points. After elucidating the MFEP network, we analysed the structures of the EQ points and the MFEPs connecting beta-sheet structures and beta-turn structures or left-handed helix structures. [ABSTRACT FROM AUTHOR]

A trivial flaw in the utilization of artificial neural networks in interpolating chemical potential energy surfaces (PES) whose descriptors are Cartesian coordinates is their dependence on simple translations and rotations of the molecule under consideration. A different set of descriptors can be chosen to circumvent this problem, internuclear distances, inverse internuclear distances or z‐matrix coordinates are three such descriptors. The objective is to use an interpolated PES in instanton rate constant calculations, hence information on the energy, gradient, and Hessian is required at coordinates in the vicinity of the tunneling path. Instanton theory relies on smoothly fitted Hessians, therefore we use energy, gradients, and Hessians in the training procedure. A major challenge is presented in the proper back‐transformation of the output gradients and Hessians from internal coordinates to Cartesian coordinates. We perform comparisons between our method, a previous approach and on‐the‐fly rate constant calcuations on the hydrogen abstraction from methanol and on the hydrogen addition to isocyanic acid. © 2018Wiley Periodicals, Inc. The challenge of utilizing instanton theory on interpolated potential energy surfaces, trained using a deep neural network, where energies, gradients and Hessians are required, in coordinates invariant to rotational and translational degrees of freedom, has been examined in this contribution. One of the studied reactions, shows good agreement both with existing neural network based approaches and with on‐the‐fly rate calculations based on a UCCSD(T)‐pVTZ‐F12 potential energy surface. [ABSTRACT FROM AUTHOR]

Formylglycine generating enzyme is a copper and oxygen-dependent protein, which catalyzes C-H activation, namely the transformation of peptidyl cysteine to formylglycine. No crystal structures of the enzyme containing copper were published so far. Here, we show by combinations of density functional theory with force fields in the QM/MM approach how copper can be incorporated in the enzyme based on two crystal structures containing Ag(I) and Cd(II) in place of Cu(I) and Cu(II). While we find a linear coordination for Cu(I) and a distorted octahedral environment for Cu(II) we also find the possibility of tetrahedral coordinations in both cases. This structural flexibility may allow the enzyme to catalyze the redox process and accommodate copper in both oxidation states. [ABSTRACT FROM AUTHOR]

The hydrogen abstraction reaction between H and H2S, yielding HS and H2 as products, has been studied within the framework of interstellar surface chemistry. High-temperature rate constants below 2000 K are calculated in the gas phase and are in agreement with previously reported values. Subsequently, low-temperature rate constants down to 55 K are presented for the first time that are of interest to astrochemistry, i.e., covering both bimolecular and unimolecular reaction mechanisms. For this, a so-called implicit surface model is used. In strict terms, this is a structural gas-phase model in which the restriction of the rotation in the solid state is taken into account. The calculated kinetic isotope effects are explained in terms of the difference in activation and delocalization. All rate constants are calculated at the UCCSD(T)-F12/cc-VTZ-F12 level of theory. Finally, we show that the energetics of the reaction is affected to an only small extent by the presence of H2O or H2S molecular clusters that simulate an ice surface, calculated at the MPWB1K/def2-TZVP level of theory. [ABSTRACT FROM AUTHOR]

Canonical instanton theory is known to overestimate the rate constant close to a system-dependent crossover temperature and is inapplicable above that temperature. We compare the accuracy of the reaction rate constants calculated using recent semi-classical rate expressions to those from canonical instanton theory. We show that rate constants calculated purely from solving the stability matrix for the action in degrees of freedom orthogonal to the instanton path is not applicable at arbitrarily low temperatures and use two methods to overcome this. Furthermore, as a by-product of the developed methods, we derive a simple correction to canonical instanton theory that can alleviate this known overestimation of rate constants close to the crossover temperature. The combined methods accurately reproduce the rate constants of the canonical theory along the whole temperature range without the spurious overestimation near the crossover temperature. We calculate and compare rate constants on three different reactions: H in the Müller-Brown potential, methylhydroxycarbene → acetaldehyde and H2 + OH → H + H2O. © 2017 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Salicylate 1,2-dioxygenase (SDO) was the first enzyme discovered, in the family of iron dioxygenases, to catalyze the ring cleavage of a monohydroxylated aromatic compound, salicylate, without a proton donor. Salicylate is not electron-rich like the familiar dihydroxy or aromatic substrates with an electron-donating group that are utilized in the well-known dioxygenases. SDO carries out the intramolecular C−C bond cleavage in salicylate bearing the OH and COOH groups with high regioselectivity in comparison with the extradiol and intradiol dioxygenases. The catalytic cleavage of a nonactivated substrate like salicylate that lacks an electron-donating group, also in the absence of a proton source, raises many puzzling questions about the oxy intermediates in the reaction pathway of dioxygenase enzymes in general. To answer these fundamental queries, we have investigated the full catalytic mechanism of SDO by a combination of quantum mechanics and molecular mechanics (QM/MM) calculations. Herein, our QM/MM study has several unexpected and interesting implications for the mechanistic pathway of SDO in comparison to the experimental observations. Importantly, it unravels the basis for the unexpected 'intra'-cleavage regioselectivity in SDO. Ostensibly a similar alkylperoxo intermediate is formed in SDO much like in the extradiol and intradiol dioxygenases. In stark contrast to the two diol enzymes, the O−O bond breaking leads to an unprotonated gem-hydroxy carboxylate intermediate, a paradigm analogue of the elusive gem diol intermediate. This unprotonated gem-hydroxy carboxylate intermediate exclusively dictates the C−C cleavage regiospecificity in SDO, which is unprecedented in the family of dioxygenases. It forms a seven-membered lactone species, which eventually forms the ring-cleavage final product by incorporation of two oxygen atoms in the salicylate. Thus, our computational study unravels a detailed reaction pathway of the oxidative cleavage of salicylate without a proton source by identifying the hitherto elusive intermediates in the catalytic cycle of SDO with testable predictions. Moreover, we describe the atomistic origin of the new catalytic role of Arg127 in the catalysis and regioselectivity of SDO. It also rationalizes the formation of a side product without invoking a dioxetane intermediate. This study is important from a fundamental perspective and opens up a new window in the mechanism of the family of dioxygenase enzymes. [ABSTRACT FROM AUTHOR]

Taurine/α-ketoglutarate dioxygenase is one of the most studied α-ketoglutarate-dependent dioxygenases (αKGDs), involved in several biotechnological applications. We investigated the key step in the catalytic cycle of the αKGDs, the hydrogen transfer process, by a quantum mechanics/molecular mechanics approach (B3LYP/CHARMM22). Analysis of the charge and spin densities during the reaction demonstrates that a concerted mechanism takes place, where the H atom transfer happens simultaneously with the electron transfer from taurine to the FeO cofactor. We found the quantum tunneling of the hydrogen atom to increase the rate constant by a factor of 40 at 5 °C. As a consequence, a quite high kinetic isotope effect close to 60 is obtained, which is consistent with the experimental value. [ABSTRACT FROM AUTHOR]

Quantum mechanical tunneling of atoms is increasingly found to play an important role in many chemical transformations. Experimentally, atom tunneling can be indirectly detected by temperature-independent rate constants at low temperature or by enhanced kinetic isotope effects. In contrast, the influence of tunneling on the reaction rates can be monitored directly through computational investigations. The tunnel effect, for example, changes reaction paths and branching ratios, enables chemical reactions in an astrochemical environment that would be impossible by thermal transition, and influences biochemical processes. [ABSTRACT FROM AUTHOR]

Der quantenmechanische Tunneleffekt von Atomen wird immer häufiger als wichtiger Aspekt in chemischen Reaktionen identifiziert. Experimentell kann man Atomtunneln nur indirekt nachweisen; beispielsweise durch temperaturunabhängige Reaktionsgeschwindigkeitskonstanten oder durch sehr große kinetische Isotopeneffekte. Im Gegensatz dazu können theoretische Methoden den Einfluss des Tunneleffekts auf die Reaktionsgeschwindigkeit direkt bestimmen. Der Tunneleffekt ändert beispielsweise Reaktionspfade und Verzweigungsverhältnisse, ermöglicht chemische Reaktionen in astrochemischer Umgebung, die thermisch nicht stattfinden, und beeinflusst auch biochemische Prozesse. Der quantenmechanische Tunneleffekt von Atomen wird zunehmend als wichtiger Aspekt chemischer Reaktionen wahrgenommen. Während er experimentell nur indirekt zugänglich ist, erlauben theoretische Simulationen eine direkte Beobachtung des Tunneleffekts. Hier wird sein Einfluss auf Reaktionspfade, Verzweigungsverhältnisse, biochemische Prozesse und die Erhöhung der Reaktionsgeschwindigkeit beleuchtet, die manche Reaktionen in der Astrochemie erst ermöglicht. [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]

Salicylat ‐ 1,2 ‐ Dioxygenase (SDO) ist das erste bekannte Enzym, das die oxidative Spaltung eines einfach hydroxylierten Aromaten, Salicylat, statt der wohlbekannten elektronenreichen Substrate katalysiert. Wir haben den Mechanismus der Sauerstoffaktivierung in SDO mit QM/MM ‐ Simulationen untersucht. Unsere Ergebnisse zeigen, dass das Nicht ‐ Häm ‐ FeII ‐ Zentrum in SDO Salicylat und O2 gemeinsam durch eine starke kovalente Wechselwirkung aktiviert, um die reduktive Spaltung von O2 zu ermöglichen. Die reaktive Sauerstoffspezies ist ein kovalenter Salicylat ‐ FeII ‐ O2 ‐ Komplex, wobei die Elektronenstruktur zwischen den beiden Grenzfällen FeII ‐ O2 und FeII ‐ O2.− mit partiellem Elektronentransfer vom aktivierten Salicylat zu O2 über das Fe ‐ Zentrum liegt. Folglich verwendet SDO eine synergetische Strategie der Substrat ‐ und Sauerstoffaktivierung, um die katalytische Reaktion auszuführen, die einmalig in der Familie der Eisendioxygenasen ist. Darüber hinaus erfolgt die O2 ‐ Aktivierung in SDO ohne die Hilfe einer Protonenquelle. Unsere Studie zeigt eine bisher unbekannte Möglichkeit für den Mechanismus der O2 ‐ Aktivierung. Das Nicht ‐ Häm ‐ FeII ‐ Zentrum in Salicylat ‐ 1,2 ‐ Dioxygenase (SDO) aktiviert Salicylat und O2 synergetisch durch eine starke kovalente Wechselwirkung, wie QM/MM ‐ Simulationen der SDO zeigen. Die reaktive Sauerstoffspezies ist ein kovalenter Salicylat ‐ FeII ‐ O2 ‐ Komplex, und die O2 ‐ Aktivierung erfolgt ohne die Hilfe einer Protonenquelle. [ABSTRACT FROM AUTHOR]

In the reactions with NaN SB 3 sb , NaOAc, NaCl and H SB 2 sb O, the formation of the respective substitution products was detected by SP 1 sp H NMR spectroscopy and mass spectrometry of the reaction solution. SP 1 sp H NMR (400 MHz, CDCl SB 3 sb ): = 7.39-7.31 (m, 3 H, Ar- I H i ), 7.22-7.20 (m, 2 H, Ar- I H i ), 4.04-4.00 (m, 1 H, PhC I H i CO), 3.21 (dd, I J i = 18.6, 9.3 Hz, 1 H, C I H i HCO), 2.81 (dd, I J i = 18.6, 3.6 Hz, 1 H, CH I H i CO). SP 1 sp H NMR (400 MHz, DMSO- I d i SB 6 sb ): = 11.47 (bs, 1 H, N I H i ), 7.51-7.29 (m, 5 H, Ar- I H i ), 3.06 (d, I J i = 18.0 Hz, 1 H, C I H i HCO), 2.94 (d, I J i = 18.0 Hz, 1 H, CH I H i CO). SP 1 sp H NMR (400 MHz, CDCl SB 3 sb ): = 8.48 (bs, 1 H, N I H i ), 7.43-7.37 (m, 5 H, Ar- I H i ), 3.23 (d, I J i = 18.4 Hz, 1 H, C I H i HCO), 3.10 (d, I J i = 18.4 Hz, 1 H, CH I H i CO). [Extracted from the article]

We implemented a geometry optimizer based on Gaussian process regression (GPR) to find minimum structures on potential energy surfaces. We tested both a two times differentiable form of the Matérn kernel and the squared exponential kernel. The Matérn kernel performs much better. We give a detailed description of the optimization procedures. These include overshooting the step resulting from GPR in order to obtain a higher degree of interpolation vs. extrapolation. In a benchmark against the Limited-memory Broyden–Fletcher–Goldfarb–Shanno optimizer of the DL-FIND library on 26 test systems, we found the new optimizer to generally reduce the number of required optimization steps. [ABSTRACT FROM AUTHOR]

Nitrogenase converts gaseous dinitrogen into biologically accessible ammonia. The binding of N2 to a reduced and protonated form of the FeMo-cofactor of nitrogenase including its central carbon ligand was investigated by means of density functional calculations. It was found the central ligand to stabilize the cluster. N2 can associate to iron or molybdenum with iron being the preferred binding site. While endo and exo binding modes were investigated the exo modes are more stable. Implications on the mechanism of N2 reduction are discussed. [ABSTRACT FROM AUTHOR]

Quantum mechanical tunneling of atoms allows chemical reactions to proceed through barriers too high for thermally activated processes. This causes hydroxycarbenes to decay rapidly and at a temperature-independent rate even at 11 K. In methylhydroxycarbene, tunneling causes decay through a mechanism that reveals a high but thin barrier rather than an alternative with a lower but broader barrier. No accurate estimates of the widths of such barriers and the lengths of tunneling paths were available. Herein, such a measure is provided by calculating the length of the tunneling paths by using instanton theory. Potential energies are provided by density functional theory verified by explicitly correlated coupled cluster CCSD(T) energies. Our results explain the decay efficiency in the known cases and suggest new substitutions to tune the effects of barrier widths and heights. Fluorination and replacement of the hydroxyl group by a thiol group change the qualitative character of the decay. Methylaminocarbene is predicted to be stable for thousands of years. [ABSTRACT FROM AUTHOR]

The acquisition of labels for supervised learning can be expensive. To improve the sample efficiency of neural network regression, we study active learning methods that adaptively select batches of unlabeled data for labeling. We present a framework for constructing such methods out of (network-dependent) base kernels, kernel transformations, and selection methods. Our framework encompasses many existing Bayesian methods based on Gaussian process approximations of neural networks as well as non-Bayesian methods. Additionally, we propose to replace the commonly used last-layer features with sketched finite-width neural tangent kernels and to combine them with a novel clustering method. To evaluate different methods, we introduce an open-source benchmark consisting of 15 large tabular regression data sets. Our proposed method outperforms the state-of-the-art on our benchmark, scales to large data sets, and works out-of-the-box without adjusting the network architecture or training code. We provide open-source code that includes efficient implementations of all kernels, kernel transformations, and selection methods, and can be used for reproducing our results. [ABSTRACT FROM AUTHOR]

The radical mechanism of the conversion of glutamate to methylaspartate catalyzed by glutamate mutase is studied with quantum mechanical/molecular mechanical (QM/MM) simulations based on density functional theory (DFT/MM). The hydrogen transfer between the substrate and the cofactor is found to be rate limiting with a barrier of 101.1 kJ mol-1. A careful comparison to the uncatalyzed reaction in water is performed. The protein influences the reaction predominantly electrostatically and to a lesser degree sterically. Our calculations shed light on the atomistic details of the reaction mechanism. The well-known arginine claw and Glu 171 (Clostridium cochlearium notation) are found to have the strongest influence on the reaction. However, a catalytic role of Glu 214, Lys 322, Gln 147, Glu 330, Lys 326, and Met 294 is found as well. The arginine claw keeps the intermediates in place and is probably responsible for the enantioselectivity. Glu 171 temporarily accepts a proton from the glutamyl radical intermediate and donates it back at the end of the reaction. We relate our results to experimental data when available. Our simulations lead to further understanding of how glutamate mutase catalyzes the carbon skeleton rearrangement of glutamate. [ABSTRACT FROM AUTHOR]

We report potential-energy and free-energy data for three enzymatic reactions: carbon–halogen bond formation in fluorinase, hydrogen abstraction from camphor in cytochrome P450cam, and chorismate-to-prephenate Claisen rearrangement in chorismate mutase. The results were obtained by combined quantum mechanics/molecular mechanics (QM/MM) optimizations and two types of QM/MM free-energy simulations (free-energy perturbation and umbrella sampling) using semi-empirical or density-functional QM methods. Based on these results and our previously published free-energy data on electrophilic substitution in para-hydroxybenzoate hydroxylase, we discuss the importance of finite-temperature effects in the chemical step of enzyme reactions. We find that the entropic contribution to the activation barrier is generally rather small, usually of the order of 5 kJ mol–1 or less, consistent with the notion that enzymes bind and pre-organize the reactants in the active site. A somewhat larger entropic contribution is encountered in the case of chorismate mutase where the pericyclic transition state is intrinsically more rigid than the chorismate reactant (also in the enzyme). The present results suggest that barriers from QM/MM geometry optimization may often be close to free-energy barriers for the chemical step in enzymatic reactions. [ABSTRACT FROM AUTHOR]

Abstract: Epidermal growth factor receptor (EGFR; ErbB1, HER1 in humans) is a receptor tyrosine kinase triggering signals across the plasma membranes of cells to determine cell fate. We have used molecular dynamics simulations to investigate structural models of ErbB1 ectodomains. We show that, with minor rearrangements, the ErbB1 back-to-back dimer can align almost flat on the cell membrane. This is in contrast to the traditional picture of ErbB1 dimers standing proud of the membrane, but in line with recent FRET and EM experiments. Interaction with the membrane leads to conformational changes in the dimer, which further stabilize the back-to-back interface. On the membrane, two dimers can associate forming a tetramer. This is enabled by a head-to-head interface, involving the ligand binding side of the ectodomain, and which significantly enhances ligand binding. A weak head-to-head interface has been seen in crystal structures, but is found to stabilise appreciably in our simulation. We also find that the domains IV, connecting the receptor to the membrane, weakly interact with each other. These simulations illustrate some of the flexibility of the ErbB1 ectodomains, and may help to explain recent experimental results. [Copyright &y& Elsevier]

Biological nitrogen fixation has been investigated beginning with the monoprotonated dinitrogen bound to the FeMo cofactor of nitrogenase up to the formation of the two ammonia molecules. The energy differences of the relevant intermediates, the reaction barriers, and potentially relevant side branches are presented. During the catalytic conversion, nitrogen bridges two Fe atoms of the central cage, replacing a sulfur bridge present before dinitrogen binds to the cofactor. A transformation from cis- to trans-diazene has been found. The strongly exothermic cleavage of the dinitrogen bond takes place, while the Fe atoms are bridged by a single nitrogen atom. The dissociation of the second ammonia from the cofactor is facilitated by the closing of the sulfur bridge following an intramolecular proton transfer. This closes the catalytic cycle. [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 vibrational spectra of simple C H 3 + —Rg (Rg = He, Ne, Ar, Kr) complexes have been studied by vibrational configuration interaction theory relying on multidimensional potential energy surfaces (PESs) obtained from explicitly correlated coupled cluster calculations, CCSD(T)-F12a. In agreement with experimental results, the series of rare gas atoms leads to rather unsystematic results and indicates huge zero point vibrational energy effects for the helium complex. In order to study these sensitive complexes more consistently, we also introduce configuration averaged vibrational self-consistent field theory, which is a generalization of standard vibrational self-consistent field theory to several configurations. The vibrational spectra of the complexes are compared to that of the methyl cation, for which corrections due to scalar-relativistic effects, high-order coupled-cluster terms, e.g., quadruple excitations, and core-valence correlation have explicitly been accounted for. The occurrence of tunneling splittings for the vibrational ground-state of C H 3 + —He has been investigated on the basis of semiclassical instanton theory. These calculations and a direct comparison of the energy profiles along the intrinsic reaction coordinates with that of the hydronium cation, H3O+, suggest that tunneling effects for vibrationally excited states should be very small. [ABSTRACT FROM AUTHOR]

MLL3, also known as KMT2C, is a lysine mono-methyltransferase in charge of the writing of an epigenetic mark on lysine 4 from histone 3. The catalytic site of MLL3 is composed of four tyrosines, namely, Y44, Y69, Y128, and Y130. Tyrosine residues are highly conserved among lysine methyltransferases' catalytic sites, although their complete function is still unclear. The exploration of how modifications on these residues from the enzymatic machinery impact the enzymatic activity of MLL3 could shed light transversally into the inner functioning of enzymes with similar characteristics. Through the use of QMMM calculations, we focus on the effect of the mutation of each tyrosine from the catalytic site on the enzymatic activity and the product specificity in the current study. While we found that the mutations of Y44 and Y128 by phenylalanine inactivated the enzyme, the mutation of Y128 by alanine reactivated the enzymatic activity of MLL3. Moreover, according to our models, the Y128A mutant was even found to be capable of di- and tri-methylate lysine 4 from histone 3, what would represent a gain of function mutation, and could be responsible for the development of diseases. Finally, we were able to establish the inactivation mechanism, which involved the use of Y130 as a water occlusion structure, whose conformation, once perturbed by its mutation or Y128 mutant, allows the access of water molecules that sequester the electron pair from lysine 4 avoiding its methylation process and, thus, increasing the barrier height. [ABSTRACT FROM AUTHOR]

Microcanonical instanton theory offers the promise of providing rate constants for chemical reactions including quantum tunneling of atoms over the whole temperature range. We discuss different rate expressions, which require the calculation of stability parameters of the instantons. The traditional way of obtaining these stability parameters is shown to be numerically unstable in practical applications. We provide three alternative algorithms to obtain such stability parameters for non-separable systems, i.e., systems in which the vibrational modes perpendicular to the instanton path couple to movement along the path. We show the applicability of our algorithms on two molecular systems: H2 + OH → H2O + H using a fitted potential energy surface and HNCO + H → NH2CO using a potential obtained on-the-fly from density functional calculations. [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]

The diffusion of atoms and radicals on interstellar dust grains is a fundamental ingredient for predicting accurate molecular abundances in astronomical environments. Quantitative values of diffusivity and diffusion barriers usually rely heavily on empirical rules. In this paper, we compute the diffusion coefficients of adsorbed nitrogen atoms by combining machine learned interatomic potentials, metadynamics, and kinetic Monte Carlo simulations. With this approach, we obtain a diffusion coefficient of nitrogen atoms on the surface of amorphous solid water of merely |$(3.5 \pm 1.1)\, \times 10^{-34}$|  cm2 s−1 at 10 K for a bare ice surface. Thus, we find that nitrogen, as a paradigmatic case for light and weakly bound adsorbates, is unable to diffuse on bare amorphous solid water at 10 K. Surface coverage has a strong effect on the diffusion coefficient by modulating its value over 9–12 orders of magnitude at 10 K and enables diffusion for specific conditions. In addition, we have found that atom tunnelling has a negligible effect. Average diffusion barriers of the potential energy surface (2.56 kJ mol−1) differ strongly from the effective diffusion barrier obtained from the diffusion coefficient for a bare surface (6.06 kJ mol−1) and are, thus, inappropriate for diffusion modelling. Our findings suggest that the thermal diffusion of N on water ice is a process that is highly dependent on the physical conditions of the ice. [ABSTRACT FROM AUTHOR]

Dynamics of adsorption and desorption of (4S)-N on amorphous solid water are analysed using molecular dynamic simulations. The underlying potential energy surface was provided by machine-learned interatomic potentials. Binding energies confirm the latest available theoretical and experimental results. The nitrogen sticking coefficient is close to unity at dust temperatures of 10 K but decreases at higher temperatures. We estimate a desorption time-scale of 1 μ s at 28 K. The estimated time-scale allows chemical processes mediated by diffusion to happen before desorption, even at higher temperatures. We found that the energy dissipation process after a sticking event happens on the picosecond time-scale at dust temperatures of 10 K, even for high energies of the incoming adsorbate. Our approach allows the simulation of large systems for reasonable time-scales at an affordable computational cost and ab initio accuracy. Moreover, it is generally applicable for the study of adsorption dynamics of interstellar radicals on dust surfaces. [ABSTRACT FROM AUTHOR]

The accuracy of the training data limits the accuracy of bulk properties from machine-learned potentials. For example, hybrid functionals or wave-function-based quantum chemical methods are readily available for cluster data but effectively out of scope for periodic structures. We show that local, atom-centered descriptors for machine-learned potentials enable the prediction of bulk properties from cluster model training data, agreeing reasonably well with predictions from bulk training data. We demonstrate such transferability by studying structural and dynamical properties of bulk liquid water with density functional theory and have found an excellent agreement with experimental and theoretical counterparts. [ABSTRACT FROM AUTHOR]

Many organic co-solutes are known to stabilize or to destabilize native structures of proteins or DNA. Most of these effects can be explained by co-solute binding or exclusion mechanisms. A beneficial approach to study the underlying principles relies on the computation of Kirkwood-Buff integrals, which can be also used to derive detailed expressions for transfer free energies and changes of the chemical equilibrium between the unfolded and the native states. In this article, we use the framework of Kirkwood-Buff theory in order to study the influence of ectoine on the stability of short DNA hairpins. Our results highlight a strong binding of ectoine, which reveals a pronounced destabilization of DNA in good agreement with experimental findings. [ABSTRACT FROM AUTHOR]

The first neutral and cationic Mo imido alkylidene cyclic alkyl amino carbene (CAAC) complexes of the general formulae [Mo(N−Ar)(CHCMe2Ph)(X)2(CAAC)] and [Mo(N−Ar)(CHCMe2Ph)(X)(CAAC)][B(ArF)4] (X=Br, Cl, OTf, OC6F5; CAAC=1‐(2,6‐iPr2‐C6H3)‐3,3,5,5‐tetramethyltetrahydropyrrol‐2‐ylidene) have been synthesized from molybdenum imido bishalide alkylidene DME precursors. Different combinations of the imido and "X" ligands have been employed to understand synthetic peculiarities. Selected complexes have been characterized by single‐crystal X‐ray analysis. Due to the pronounced σ‐donor/π‐acceptor characteristics of CAACs, the corresponding neutral and cationic molybdenum imido alkylidene CAAC complexes do not require the presence of stabilizing donor ligands such as nitriles. Calculations on the PBE0‐D3BJ/def2‐TZVP level for PBE0‐D3BJ/def2‐SVP optimized geometries revealed partial charges at molybdenum similar to the corresponding molybdenum imido alkylidene N‐heterocyclic carbene (NHC) complexes with a slightly higher polarization of the molybdenum alkylidene bond in the CAAC complexes. All cationic complexes have been tested in olefin metathesis reactions and showed improved activity compared to the analogous NHC complexes for hydrocarbon‐based substrates, allowing for turnover numbers (TONs) up to 9500 even at room temperature. Some Mo imido alkylidene CAAC complexes are tolerant towards functional groups like thioethers and sulfonamides. [ABSTRACT FROM AUTHOR]

Pyrazolones represent an important structural motif in active pharmaceutical ingredients. Their asymmetric synthesis is thus widely studied. Still, a generally highly enantio‐ and diastereoselective 1,4‐addition to nitroolefins providing products with adjacent stereocenters is elusive. In this article, a new polyfunctional CuII‐1,2,3‐triazolium‐aryloxide catalyst is presented which enables this reaction type with high stereocontrol. DFT studies revealed that the triazolium stabilizes the transition state by hydrogen bonding between C(5)−H and the nitroolefin and verify a cooperative mode of activation. Moreover, they show that the catalyst adopts a rigid chiral cage/pore structure by intramolecular hydrogen bonding, by which stereocontrol is achieved. Control catalyst systems confirm the crucial role of the triazolium, aryloxide and CuII, requiring a sophisticated structural orchestration for high efficiency. The addition products were used to form pyrazolidinones by chemoselective C=N reduction. These heterocycles are shown to be valuable precursors toward β,γ'‐diaminoamides by chemoselective nitro and N−N bond reductions. Morphological profiling using the Cell painting assay identified biological activities for the pyrazolidinones and suggest modulation of DNA synthesis as a potential mode of action. One product showed biological similarity to Camptothecin, a lead structure for cancer therapy. [ABSTRACT FROM AUTHOR]

Pyrazolone repräsentieren ein strukturell wichtiges Motiv in vielen Wirkstoffen. Ihre asymmetrische Synthese ist daher gut untersucht. Trotzdem ist eine enantio‐ sowie diastereoselektive 1,4‐Addition an Nitroolefine, die Produkte mit benachbarten Stereozentren bildet, kaum bekannt. In diesem Artikel wird ein neuartiger, polyfunktioneller CuII‐1,2,3‐Triazolium‐Aryloxid‐Katalysator vorgestellt, der diese Reaktion mit hoher Stereokontrolle ermöglicht. DFT‐Studien zeigen hierbei, dass die Triazolium‐Einheit den Übergangszustand durch eine Wasserstoffbrücke des C(5)−H zum Nitroolefin stabilisiert, was die polyfunktionelle Aktivierung durch dieses System belegt. Weiterhin zeigt sich, dass der Katalysator durch eine intramolekulare Wasserstoffbrücke eine starre Käfig‐/ Poren‐Struktur ausbildet, wodurch Stereokontrolle erlangt wird. Kontrollsysteme in der Katalyse bestätigen hierbei die essenzielle Rolle des Triazoliums, Aryloxids sowie CuII, welche eine ausgeklügelte strukturelle Orchestrierung benötigen, um hoch effizient zu arbeiten. Die Additionsprodukte wurden verwendet um Pyrazolidinone durch chemoselektive C=N‐Reduktion zu bilden. Diese Heterozyklen konnten als Vorstufen zur Synthese von β,γ'‐Diaminoamiden durch chemoselektive Nitro‐ und N,N‐Bindungsreduktion genutzt werden. Morphologisches Profiling mittels Cell Painting Assay konnte die biologische Aktivität der Pyrazolidinone aufzeigen, wobei die Regulierung der DNA‐Synthese als potenzielle Wirkungsweise identifiziert wurde. Ein Produkt zeigte hierbei biologische Ähnlichkeit zu Camptothecin, einer Leitstruktur in der Krebstherapie. [ABSTRACT FROM AUTHOR]

Abstract: Fluoroacetate dehalogenase is able to cleavage a carbon–fluoride bond, the strongest carbon–halogen bond in nature, in a process initiated by a SN2 reaction. The role of the enzyme machinery and particularly of the halogen pocket in the SN2 reaction is thoroughly explored by using state‐of‐the‐art computational tools. A comparison between the non‐catalyzed versus enzyme‐catalyzed reaction, as well as with a mutant of the enzyme (Tyr219Phe), is presented. The energy barrier changes are rationalized by means of reaction force analysis and the activation strain model coupled with energy decomposition analysis. The catalysis is in part caused by the reduction of structural work from bringing the reactant species towards the proper reaction orientation, and the reduction of the electrostatic repulsion between the nucleophile and the substrate, which are both negatively charged. In addition, catalysis is also driven by an important reduction of the electronic reorganization processes during the reaction, where Tyr from the halogen pocket acts as a charge acceptor from the SN2 reaction axis therefore reducing the electronic steric repulsion between the reacting parts. [ABSTRACT FROM AUTHOR]

Oxford University Press, 2013. 304 pp., hardcover, $ 19.95.—ISBN 978‐0195391312 [ABSTRACT FROM AUTHOR]

Oxford University Press, 2013. 304 S., geb., 19.95 $.—ISBN 978 ‐ 0195391312 [ABSTRACT FROM AUTHOR]

Hydroxylamine, NH2OH, is one of the already detected interstellar molecules with the highest prebiotic potential. Yet, the abundance of this molecule found by astronomical observations is rather low for a relatively simple molecule, ∼10−10 relative to H2. This seemingly low abundance can be rationalized by destruction routes operating on interstellar dust grains. In this work, we tested the viability of this hypothesis under several prisms, finding that the origin of a lower abundance of NH2OH can be explained by two chemical processes, one operating at low temperature (10 K) and the other at intermediate temperature (20 K). At low temperatures, enabling the hydrogen abstraction reaction HNO + H → NO + H2, even in small amounts, partially inhibits the formation of NH2OH through successive hydrogenation of NO, and reduces its abundance on the grains. We found that enabling a 15–30  per cent of binding sites for this reaction results in reductions of NH2OH abundance of approximately one to two orders of magnitude. At warmer temperatures (20 K, in our study), the reaction NH2OH + H → HNOH + H2, which was found to be fast (k ∼ 106 s−1) in this work, followed by further abstractions by adsorbates that are immobile at 10 K (O, N) are the main route of NH2OH destruction. Our results shed light on the abundance of hydroxylamine in space and pave the way to constraining the subsequent chemistry experienced by this molecule and its derivatives in the interstellar prebiotic chemistry canvas. [ABSTRACT FROM AUTHOR]

For decades there were many attempts to dispense with stoichiometric amounts of metal reagents for the synthesis of secondary alcohols. In 2021, the synthetic results of Newman and collaborators pioneered a synthesis still with metals, but not as reactants. Instead, they serverd as catalytic engines. Here we present a description by means of Density Functional Theory calculations of how this process can occur, and an attempt is made to shed light on the mechanism that facilitates the attainment of secondary alcohols, emphasizing the eternal cross‐coupling debate of whether the catalytically active species is Ni(0) or they are really taking shortcuts following the course of Ni(II). Effective Orbital analyses give a clear picture. Furthermore, this paper provides insight not only into the nature of the ligands of the metal catalyst but also the role of the base. [ABSTRACT FROM AUTHOR]

While ZrO2 is known to have a large effect on the activity and selectivity of the Cu/ZrO2 catalyst for methanol synthesis, its role in this process is poorly understood. Surface defects such as oxygen vacancies could play a role in the strong metal‐support interaction (SMSI) between Cu and ZrO2. However, due to the complexity of the surfaces, the exact molecular nature of this interaction is not at present known. Here, we make well‐defined models of both reduced and coordinatively unsaturated surface oxygen vacancies on ZrO2 using the molecular precursor [Cp2ZrCl]2(μ2‐O) (1). Complex 1 can be reduced to form a complex (2) containing one Zr(III) center and a bridging hydride ligand (according to EPR and IR spectroscopy) derived from C−H activation of either thf or the Cp ring. Complex 2 reacts with CO2 to largely produce CO, suggesting that surface defects with similar structures probably do not play a role in the industrial catalyst. Halide abstraction from complex 1 results in the Lewis acidic species 3, which has similar Lewis acid properties to acidic defects on the ZrO2 surface. Similarities of both of these model species to real surface oxygen vacancies and their role in the catalytic reaction are discussed. [ABSTRACT FROM AUTHOR]

A catalyst type is disclosed allowing for exceptional efficiency in direct 1,4‐additions. The catalyst is a zwitterionic entity, in which acetate binds to CuII, which is formally negatively charged and serving as counterion for benzimidazolium. All 3 functionalities are involved in the catalytic activation. For maleimides productivity was increased by a factor >300 compared to literature (TONs up to 6700). High stereoselectivity and productivity was attained for a broad range of other Michael acceptors as well. The polyfunctional catalyst is accessible in only 4 steps from N‐Ph‐benzimidazole with an overall yield of 96 % and robust during catalysis. This allowed to reuse the same catalyst multiple times with nearly constant efficiency. Mechanistic studies, in particular by DFT, give a detailed picture how the catalyst operates. The benzimidazolium unit stabilizes the coordinated enolate nucleophile and prevents that acetate/acetic acid dissociate from the catalyst. [ABSTRACT FROM AUTHOR]

Ein Katalysatortyp wird vorgestellt, der eine außergewöhnliche Effizienz bei direkten 1,4‐Additionen ermöglicht. Der Katalysator ist eine zwitterionische Einheit, in der Acetat an CuII bindet, das formal negativ geladen ist und als Gegenion für eine Benzimidazolium‐Einheit dient. Alle 3 Funktionalitäten sind an der katalytischen Aktivierung beteiligt. Für Maleimide wurde die Produktivität im Vergleich zur Literatur um einen Faktor >300 gesteigert (Umsatzzahlen bis zu 6700). Eine hohe Stereoselektivität und Produktivität wurde auch für ein breites Spektrum anderer Michael‐Akzeptoren erreicht. Der polyfunktionelle Katalysator ist in nur 4 Stufen ausgehend von N−Ph‐Benzimidazol mit einer Gesamtausbeute von 96 % zugänglich und stabil während der Katalyse. Dies ermöglichte die mehrfache Wiederverwendung des gleichen Katalysators mit nahezu konstanter Effizienz. Mechanistische Studien, insbesondere durch DFT, liefern ein detailliertes Bild der Funktionsweise des Katalysators. Die Benzimidazolium‐Einheit stabilisiert das koordinierte Enolat‐Nucleophil und verhindert, dass Acetat/Essigsäure vom Katalysator dissoziieren. [ABSTRACT FROM AUTHOR]

Artificial neural networks are used to fit a potential energy surface (PES). We demonstrate the benefits of using not only energies but also their first and second derivatives as training data for the neural network. This ensures smooth and accurate Hessian surfaces, which are required for rate constant calculations using instanton theory. Our aim was a local, accurate fit rather than a global PES because instanton theory requires information on the potential only in the close vicinity of the main tunneling path. Elongations along vibrational normal modes at the transition state are used as coordinates for the neural network. The method is applied to the hydrogen abstraction reaction from methanol, calculated on a coupled-cluster level of theory. The reaction is essential in astrochemistry to explain the deuteration of methanol in the interstellar medium. [ABSTRACT FROM AUTHOR]