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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]

Water is one of the most abundant molecules in the form of solid ice phase in the different regions of the interstellar medium (ISM). This large abundance cannot be properly explained by using only traditional low-temperature gas-phase reactions. Thus, surface chemical reactions are believed to be major synthetic channels for the formation of interstellar water ice. Among the different proposals, hydrogenation of atomic O (i.e. 2H  + O → H2O) is a chemically 'simple' and plausible reaction toward water formation occurring on the surfaces of interstellar grains. Here, novel theoretical results concerning the formation of water adopting this mechanism on the crystalline (010) Mg2SiO4 surface (a unequivocally identified interstellar silicate) are presented. The investigated reaction aims to simulate the formation of the first water ice layer covering the silicate core of dust grains. Adsorption of the atomic O as a first step of the reaction has been computed, results indicating that a peroxo (O |$^{2-}_{2}$|⁠) group is formed. The following steps involve the adsorption, diffusion, and reaction of two successive H atoms with the adsorbed O atom. Results indicate that H diffusion on the surface has barriers of 4–6 kcal mol−1, while actual formation of OH and H2O present energy barriers of 22–23 kcal mol−1. Kinetic study results show that tunneling is crucial for the occurrence of the reactions and that formation of OH and H2O are the bottlenecks of the overall process. Several astrophysical implications derived from the theoretical results are provided as concluding remarks. [ABSTRACT FROM AUTHOR]

Rate constants for the radical-induced hydrogen abstraction from formic acid, HCOOH, are presented here. Only those reactions leading to the formation of HOCO were investigated. The astrochemically relevant radicals OH, NH2, and H were considered to induce the H-abstraction. Tunnelling was taken into account by using the instanton method for rate constant calculations. For reactions relevant on grain surfaces, the unimolecular rate constant is of particular importance. For the reactions with OH and NH2, a corresponding deep pre-reactive minimum can be found that contributes to the barrier height and thus slows down the reaction. In general though, abstraction induced by OH radicals is found to be the fastest. The reaction with the H atoms becomes increasingly important at low temperatures, because of the narrow barrier through which tunnelling is efficient. The reaction with NH2 radicals has both a high and broad barrier and consequently shows significantly smaller low-temperature rate constants. [ABSTRACT FROM AUTHOR]

Abstract: Isoxazolinones are biologically and synthetically interesting densely functionalized heterocycles, which for a long time were not accessible in enantioenriched form by asymmetric catalysis. Next to the deficit of enantioselective methods, the functionalization of isoxazolinones is often plagued by regioselectivity issues due to the competition of various nucleophilic centers within the heterocycles. We report the first regio‐ and enantioselective C‐allylations of isoxazolinones. These occur with high regioselectivity in favor of the linear allylation products, although Ir phosphoramidite catalysts were used, which commonly results in branched isomers. Our studies suggest that this outcome is the result of a reaction cascade via an initial regio‐ and enantioselective N‐allylation to provide a branched allyl intermediate, followed by a spontaneous [3,3]‐rearrangement resulting in chirality transfer. [ABSTRACT FROM AUTHOR]

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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]

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]

Investigating how formamide forms in the interstellar medium is a hot topic in astrochemistry, which can contribute to our understanding of the origin of life on Earth. We have constructed a QM/MM model to simulate the hydrogenation of isocyanic acid on amorphous solid water surfaces to form formamide. The binding energy of HNCO on the ASW surface varies significantly between different binding sites, we found values between ∼0 and 100 kJ mol−1. The barrier for the hydrogenation reaction is almost independent of the binding energy, though. We calculated tunneling rate constants of H + HNCO → NH2CO at temperatures down to 103 K combining QM/MM with instanton theory. Tunneling dominates the reaction at such low temperatures. The tunneling reaction is hardly accelerated by the amorphous solid water surface compared to the gas phase for this system, even though the activation energy of the surface reaction is lower than the one of the gas-phase reaction. Both the height and width of the barrier affect the tunneling rate in practice. Strong kinetic isotope effects were observed by comparing to rate constants of D + HNCO → NHDCO. At 103 K we found a KIE of 231 on the surface and 146 in the gas phase. Furthermore, we investigated the gas-phase reaction NH2 + H2CO → NH2CHO + H and found it unlikely to occur at cryogenic temperatures. The data of our tunneling rate constants are expected to significantly influence astrochemical models. [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]