Search

Chemical processes taking place on ice-grain mantles are pivotal to the complex chemistry of interstellar environments. In this study, we conducted a comprehensive analysis of the catalytic effects of an amorphous solid water (ASW) surface on the reaction between ammonia (NH 3 ) and formaldehyde (H 2 CO) to form aminomethanol (NH 2 CH 2 OH) using density functional theory. We identified potential catalytic sites based on the binding energy distribution of NH 3 and H 2 CO reactants, on a set-of-clusters surface model composed of 22 water molecules and found a total of 14 reaction paths. Our results indicate that the catalytic sites can be categorized into four groups, depending on the interactions of the carbonyl oxygen and the amino group with the ice surface in the reactant complex. A detailed analysis of the reaction mechanism using Intrinsic Reaction Coordinate and reaction force analysis, revealed three distinct chemical events for this reaction: formation of the C-N bond, breaking of the N-H bond, and formation of the O-H hydroxyl bond. Depending on the type of catalytic site, these events can occur within a single, concerted, albeit asynchronous, step, or can be isolated in a step-wise mechanism, with the lowest overall transition state energy observed at 1.3 kcal mol -1 . A key requirement for the low-energy mechanism is the presence of a pair of dangling OH bonds on the surface, found at 5% of the potential catalytic sites on an ASW porous surface.

Carboxy-biotin serves as a coenzyme in certain carboxylases, exhibiting the remarkable capability to transfer a carboxy group to specific substrates. This process is made possible by the presence of biotin, a unique molecule that consists of a sulfur-containing tetrahydrothiophene ring fused to a ureido group. It is covalently attached to the enzyme via a flexible linker, allowing for its functionality. Biotin-dependent carboxylases consist of two distinct domains. The first domain (BC) facilitates biotin carboxylation by utilizing ATP, while the second domain (CT) transfers CO 2 to the substrate. The process of ATP-dependent carboxylation using bicarbonate in the biotin carboxylase domain (BC) is well-known. However, the precise mechanism by which CO 2 is released in the carboxyltransferase domain (CT) is still not fully understood. We employed advanced computational chemistry methods to investigate the decarboxylation process of carboxy-biotin in various molecular environments and different protonation states. Regardless of the polarity of the molecular surroundings, decarboxylation only occurs spontaneously in the protonated form. To determine the protonation state of biotin in different environments, we established an accurate computational chemistry method for calculating the p K a value of carboxy-biotin, reaching sub-kcal/mol accuracy. Based on our findings, nonpolar environments, such as the active site of the carboxyltransferase domain, have the ability to cause the spontaneous release of CO 2 from carboxy-biotin. The CO 2 release takes place spontaneously from protonated carboxy-biotin, promoting the carboxylation of substrates.

Hydride transfer reactions involving 1,4-dihydropyridines play a central role in bioorganic chemistry as they represent an important share of redox metabolism. For this class of reactions, direct hydride transfer is the commonly accepted mechanism; however, an Alder-Ene-like pathway has been proposed as a plausible alternative. The reaction between 1,4-ditrimethylsilyl-1,4-dihydropyridine and α,β-unsaturated nitriles is a solid candidate for this latter pathway. In this work, we perform high level ab initio and density functional theory computations to characterize the mechanism of this reaction, taking into account diverse reaction paths, and evaluating the effect of solvent polarity and variations in the chemical structure. Our analysis explains the stereochemical aspects of the reaction, characterizing the up to now unresolved spatial configurations of the predominant products, and may contribute to the understanding of enzymatic reactions involving NADP(H). The reactions are found to proceed in an asynchronous fashion, with transition states that display significant aromatic features. With this observation in mind, Alder-Ene and direct hydride transfer pathways can be understood as two extremes of a continuous mechanistic spectrum for this kind of reaction, with the analyzed systems located approximately equidistant from both ends.

Binding affinity prediction by means of computer simulation has been increasingly incorporated in drug discovery projects. Its wide application, however, is limited by the prediction accuracy of the free energy calculations. The main error sources are force fields used to describe molecular interactions and incomplete sampling of the configurational space. Organic host-guest systems have been used to address force field quality because they share similar interactions found in ligands and receptors, and their rigidity facilitates configurational sampling. Here, we test the binding free energy prediction accuracy for 14 guests with an aromatic or adamantane core and the CB7 host using molecular electron density derived nonbonded force field parameters. We developed a computational workflow written in Python to derive atomic charges and Lennard-Jones parameters with the Minimal Basis Iterative Stockholder method using the polarized electron density of several configurations of each guest in the bound and unbound states. The resulting nonbonded force field parameters improve binding affinity prediction, especially for guests with an adamantane core in which repulsive exchange and dispersion interactions to the host dominate.

Carboxylation reactions represent a very special class of chemical reactions that is characterized by the presence of a carbon dioxide (CO 2 ) molecule as reactive species within its global chemical equation. These reactions work as fundamental gear to accomplish the CO 2 fixation and thus to build up more complex molecules through different technological and biochemical processes. In this context, a correct description of the CO 2 electronic structure turns out to be crucial to study the chemical and electronic properties associated with this kind of reactions. Here, a systematic study of CO 2 electronic structure and its contribution to different carboxylation reaction electronic energies has been carried out by means of several high-level ab initio post-Hartree Fock (post-HF) and density functional theory (DFT) calculations for a set of biochemistry and inorganic systems. We have found that for a correct description of the CO 2 electronic correlation energy it is necessary to include post-CCSD(T) contributions (beyond the gold standard). These high-order excitations are required to properly describe the interactions of the four π-electrons associated with the two degenerated π-molecular orbitals of the CO 2 molecule. Likewise, our results show that in some reactions it is possible to obtain accurate reaction electronic energy values with computationally less demanding methods when the error in the electronic correlation energy compensates between reactants and products. Furthermore, the provided post-HF reference values allowed to validating different DFT exchange-correlation functionals combined with different basis sets for chemical reactions that are relevant in biochemical CO 2 fixing enzymes. © 2019 Wiley Periodicals, Inc., (© 2019 Wiley Periodicals, Inc.)

Despite increasing experimental interest in aliphatic polyesters as biodegradable and bioassimilable polymers a theoretical description of ring-opening polymerization (ROP) is not yet fully established. We report a detailed theoretical account of the mechanism of the ROP of three lactones (glycolide, 1,5-dioxepan-2-one and ε-caprolactone) using dimethylaluminium methoxide (Al(CH 3 ) 2 OCH 3 ) as the initiator. Both the initiation and propagation steps of the ROP are investigated using a composite method consisting of explicitly correlated Moller-Plesset (DF-MP2-F12) and explicitly correlated local coupled cluster methods (DF-LCCSD(T)-F12), for an accurate and definitive determination of the transition state and intermediate electronic energies. A hitherto unreported transition state is found in the initiation reaction, which is the highest energy stationary state for all three lactones. Computed reaction free energies suggest a thermodynamically favourable polymerization of the ROP for all three lactones and a "living mechanism" in the cases of glycolide and 1,5-dioxepan-2-one. The intrinsic reaction coordinate analysis for the ROP of glycolide connects the different stationary states and establishes mechanistic differences between the initiation and propagation reactions. The analysis of structural and electronic parameters along the reaction coordinate reveals a decoupling of structural and electronic changes in the initiation reaction, which allows it to proceed over a lower energy path than in the propagation reaction, where no decoupling is found. Finally, the ab initio electronic energies are compared to popular DFT functionals, where it is found that PBE0 performs best among all tested functionals.

Methyl transfer reactions play an important role in biology and are catalyzed by various enzymes. Here, the influence of the molecular environment on the reaction mechanism was studied using advanced ab initio methods, implicit solvation models and QM/MM molecular dynamics simulations. Various conceptual DFT and electronic structure descriptors identified different processes along the reaction coordinate e.g. electron transfer. The results show that the polarity of the solvent increases the energy required for the electron transfer and that this spontaneous process is located in the transition state region identified by the (mean) reaction force analysis and takes place through the bonds which are broken and formed. The inclusion of entropic contributions and hydrogen bond interactions in QM/MM molecular dynamics simulations with a validated DFTB3 Hamiltonian yields activation barriers in good agreement with the experimental values in contrast to the values obtained using two implicit solvation models.

In symmetry controlled reactions, orbital degeneracies among orbitals of different symmetries can occur along a reaction coordinate. In such case Koopmans' theorem and the finite difference approximation provide a chemical potential profile with nondifferentiable points. This results in an ill-defined reaction electronic flux (REF) profile, since it is defined as the derivative of the chemical potential with respect to the reaction coordinate. To overcome this deficiency, we propose a new way for the calculation of the chemical potential based on a many orbital approach, suitable for reactions in which symmetry is preserved. This new approach gives rise to a new descriptor: symmetry adapted chemical potential (SA-CP), which is the chemical potential corresponding to a given irreducible representation of a symmetry group. A corresponding symmetry adapted reaction electronic flux (SA-REF) is also obtained. Using this approach smooth chemical potential profiles and well defined REFs are achieved. An application of SA-CP and SA-REF is presented by studying the Cs enol-keto tautomerization of thioformic acid. Two SA-REFs are obtained, JA'(ξ) and JA'' (ξ). It is found that the tautomerization proceeds via an in-plane delocalized 3-center 4-electron O-H-S hypervalent bond which is predicted to exist only in the transition state (TS) region. © 2016 Wiley Periodicals, Inc., (© 2016 Wiley Periodicals, Inc.)

With increasing computational capabilities, an ever growing amount of data is generated in computational chemistry that contains a vast amount of chemically relevant information. It is therefore imperative to create new computational tools in order to process and extract this data in a sensible way. Kudi is an open source library that aids in the extraction of chemical properties from reaction paths. The straightforward structure of Kudi makes it easy to use for users and allows for effortless implementation of new capabilities, and extension to any quantum chemistry package. A use case for Kudi is shown for the tautomerization reaction of formic acid. Kudi is available free of charge at www.github.com/stvogt/kudi.

Natural bond orbital (NBO) analyses and dissected nucleus-independent chemical shifts (NICS π z z ) were computed to evaluate the bonding (bond type, electron occupation, hybridization) and aromatic character of the three lowest-lying Si2CH2 (1-Si, 2-Si, 3-Si) and Ge2CH2 (1-Ge, 2-Ge, 3-Ge) isomers. While their carbon C3H2 analogs favor classical alkene, allene, and alkyne type bonding, these Si and Ge derivatives are more polarizable and can favor "highly electron delocalized"? and "non-classical"? structures. The lowest energy Si 2CH2 and Ge 2CH2 isomers, 1-Si and 1-Ge, exhibit two sets of 3-center 2-electron (3c-2e) bonding; a π-3c-2e bond involving the heavy atoms (C-Si-Si and C-Ge-Ge), and a σ-3c-2e bond (Si-H-Si, Ge-H-Ge). Both 3-Si and 3-Ge exhibit π and σ-3c-2e bonding involving a planar tetracoordinated carbon (ptC) center. Despite their highly electron delocalized nature, all of the Si2CH2 and Ge2CH2 isomers considered display only modest two π electron aromatic character (NICS(0) π z z =--6.2 to -8.9 ppm, computed at the heavy atom ring center) compared to the cyclic-C 3H2 (-13.3 ppm). Graphical Abstract The three lowest Si2CH2 and Ge2CH2 isomers.

In this study a systematic theoretical investigation of Ge2CH2 is carried out. The singlet potential energy surface (PES) was explored using state-of-the-art theoretical methods including self-consistent field (SCF), coupled cluster theory incorporating single and double excitation (CCSD), perturbative triple [CCSD(T)] and full triples [CCSDT] with perturbative quadruple (Q), together with a variety of correlation-consistent polarized valence basis sets cc-pVXZ (where X = D, T, and Q). A total of eleven stationary points have been located on the Ge2CH2 singlet ground state PES. Among them, seven structures are minima (1S-7S), two are transition states (TS1 and TS2), and two are second-order saddle points (SSP1 and SSP2). The global minimum is predicted to be an exotic hydrogen-bridged structure 1S. The energy ordering of the seven minima (in kcal mol(-1)) obtained from focal point analysis using the extrapolation to complete basis set (CBS) limit with zero point vibrational energy (ZPVE), core correlation, diagonal Born-Oppenheimer (DBOC) and relativistic correction is 1S [0.0] < 2S [17.2] < 3S [18.3] < 4S [31.7] < 5S [39.9] < 6S [58.1] < 7S [82.1].

The dependence of the relative energies of 116 diphosphene and diphosphinylidene compounds on the modification of their structures is studied theoretically. Optimized geometries and relative energies are reported for all structures. With the purpose of investigating the effects of various substituents on the parent PPH2 and HPPH molecules, isodesmic reaction energies were obtained for single and double substitution. In the case of the substitution of both H atoms by lithoxy (OLi) or ONa groups is the diphosphinylidene type structure found to be lower in energy. For the lithoxy group, the energy difference amounts to 33 kcal/mol at CCSD(T) cc-pVTZ level of theory. This result is explained through the natural population analyses, where a very favorable Coulombic attraction is found in the OLi substituted diphosphinylidene structure. The order of the effectiveness of the substituents in lowering the relative energy of the diphosphinylidene structure is OLi > ONa > OH > OSiH3 > OCH3 > OPh > NH2 > N(CH3)2 > F > ONH2 > OBH2 > CH3 > OOH > Ph > BF2 > PH2 > SiH3 > SH > HC═O > Cl > CF3 > Br > SiF3 > NF2 > NO2 > C≡CH > OF > CN. Natural bond orbital (NBO) analysis explains other qualitative bonding features, for example, phosphorus-phosphorus bond orders as large as 2.5 for R2PP structures and as small as 1.6 for RPPR structures.

A theoretical study of the mechanism of the isomerization reaction HOC(+) --> HCO(+) is presented. The mechanism was studied in terms of reaction force, chemical potential, reaction electronic flux (REF), and bond orders. It has been found that the evolution of changes in REF along the intrinsic reaction coordinate can be explained in terms of bond orders. The energetic lowering of the hydrogen assisted (catalyzed) reaction has been identified as being due to the stabilization of the H(3)(+) transition state complex and the stepwise bond dissociation and formation of the H-O and H-C bonds, respectively.