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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]

A quantum chemical investigation of the Bu4N[Fe(CO)3(NO)]-catalyzed Cloke-Wilson rearrangement of vinyl cyclopropanes is reported. It was found that allylic CC bond activation can proceed through a SN2′ or SN2-type mechanism. The application of the recently reported intrinsic bond orbital (IBO) method for all structures indicated that one FeN π bond is directly involved. Further analysis showed that during the reaction oxidation occurs at the NO ligand exclusively. [ABSTRACT FROM AUTHOR]

Quantum tunneling of atoms, the penetration of energy barriers higher than the total energy of the system, plays a role in many chemical systems. While any chemical reaction is dominated by tunneling at low enough temperature, there is evidence for hydrogen atom tunneling even in enzymatic reactions at ambient conditions. The smaller the mass of the atoms, the lower and thinner the barrier is, the stronger the tunneling effect increases the reaction rate. Different methods to calculate tunneling rates are available. They range from full solutions of the time-dependent Schrödinger equation via the semiclassical method to ad hoc corrections of classical transition state theory. The basis of different methods, their accuracy, and applicability is discussed in the present overview, with a particular focus on instanton theory, a Feynman-path-based approach using the semiclassical approximation. [ABSTRACT FROM AUTHOR]

ChemShell is a modular computational chemistry package with a particular focus on hybrid quantum mechanical/molecular mechanical ( QM/ MM) simulations. A core set of chemical data handling modules and scripted interfaces to a large number of quantum chemistry and molecular modeling packages underpin a flexible QM/ MM scheme. ChemShell has been used in the study of small molecules, molecular crystals, biological macromolecules such as enzymes, framework materials including zeolites, ionic solids, and surfaces. We outline the range of QM/ MM coupling schemes and supporting functions for system setup, geometry optimization, and transition-state location (including those from the open-source DL- FIND optimization library). We discuss recently implemented features allowing a more efficient treatment of long range electrostatic interactions, X-ray based quantum refinement of crystal structures, free energy methods, and excited-state calculations. ChemShell has been ported to a range of parallel computers and we describe a number of options including parallel execution based on the message-passing capabilities of the interfaced packages and task-farming for applications in which a number of individual QM, MM, or QM/ MM calculations can performed simultaneously. We exemplify each of the features by brief reference to published applications. [ABSTRACT FROM AUTHOR]

A well-studied periplasmic-binding protein involved in the abstraction of maltose is maltose-binding protein (MBP), which undergoes a ligand-induced conformational transition from an open (ligand-free) to a closed (ligand-bound) state. Umbrella sampling simulations have been us to estimate the free energy of binding of maltose to MBP and to trace the potential of mean force of the unbinding event using the center-of-mass distance between the protein and ligand as the reaction coordinate. The free energy thus obtained compares nicely with the experimentally measured value justifying our theoretical basis. Measurement of the domain angle (N-terminal-domain - hinge - C-terminal-domain) along the unbinding pathway established the existence of three different states. Starting from a closed state, the protein shifts to an open conformation during the initial unbinding event of the ligand then resides in a semi-open conformation and later resides predominantly in an open-state. These transitions along the ligand unbinding pathway have been captured in greater depth using principal component analysis. It is proposed that in mixed-model, both conformational selection and an induced-fit mechanism combine to the ligand recognition process in MBP. Proteins 2013. © 2012 Wiley Periodicals, Inc. [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]

Keywords: asymmetric catalysis; diene ligands; liquid confinement; microemulsions; rhodium-catalyzed 1,2-addition EN asymmetric catalysis diene ligands liquid confinement microemulsions rhodium-catalyzed 1,2-addition 1 1 1 12/09/21 20211206 NES 211206 B The influence of anionic and cationic co-surfactants b in nonionic microemulsions on the performance of chiral Rh-norbornadiene complexes with different counterions in the 1,2-addition of phenylboronic acids to I N i -tosylimines is described. Asymmetric catalysis, diene ligands, liquid confinement, microemulsions, rhodium-catalyzed 1,2-addition. [Extracted from the article]

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]

The mixed lineage leukemia 3 or MLL3 is the enzyme in charge of the writing of an epigenetic mark through the methylation of lysine 4 from the N-terminal domain of histone 3 and its deregulation has been related to several cancer lines. An interesting feature of this enzyme comes from its regulation mechanism, which involves its binding to an activating dimer before it can be catalytically functional. Once the trimer is formed, the reaction mechanism proceeds through the deprotonation of the lysine followed by the methyl-transfer reaction. Here we present a detailed exploration of the activation mechanism through a QM/MM approach focusing on both steps of the reaction, aiming to provide new insights into the deprotonation process and the role of the catalytic machinery in the methyl-transfer reaction. Our finding suggests that the source of the activation mechanism comes from conformational restriction mediated by the formation of a network of salt-bridges between MLL3 and one of the activating subunits, which restricts and stabilizes the positioning of several residues relevant for the catalysis. New insights into the deprotonation mechanism of lysine are provided, identifying a valine residue as crucial in the positioning of the water molecule in charge of the process. Finally, a tyrosine residue was found to assist the methyl transfer from SAM to the target lysine. [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]

Most interstellar and planetary environments are suffused by a continuous flux of several types of ionizing radiation, including cosmic rays, stellar winds, x-rays, and gamma-rays from radionuclide decay. There is now a large body of experimental work showing that these kinds of radiation can trigger significant physicochemical changes in ices, including the dissociation of species (radiolysis), sputtering of surface species, and ice heating. Even so, modeling the chemical effects that result from interactions between ionizing radiation and interstellar dust grain ice mantles has proven challenging due to the complexity and variety of the underlying physical processes. To address this shortcoming, we have developed a method whereby such effects could easily be included in standard rate-equations-based astrochemical models. Here, we describe how such models, thus improved, can fruitfully be used to simulate experiments in order to better understand bulk chemistry at low temperatures. [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 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]