For exploring the reaction between the hydroxyl groups of lignin and boric acid under the alkaline condition, we study three proposed mechanisms for the formation of the anionic borate diester (ABDE) using the salicyl alcohol anion as the model compound by the density functional theory. ABDE has high flame retardancy and is a potentially practical application of lignin. The catalysis of sodium cation is found to enhance the deprotonation of the water cluster. The deprotonated product, hydroxide anion, is essential to the critical step, which is the cleavage of B-O bonds of the boric acid molecule, in reaction mechanisms. The energy profiles of the mechanisms show that the reaction between lignin and boric acid may start from the hydroxymethyl moieties of lignin since it requires less energy for the aforementioned critical step than from the phenol moieties of lignin. Moreover, the hydroxide anions compete with the hydroxymethyl groups in lignin for the formation of B-O bonds by forming tetrahydroxyborate anion (TBA) which requires very high activation energies to further react to the desired product ABDE. The optimal condition is to enhance the catalytic effect of sodium cations and meanwhile to control the formation of TBA.

A two-pronged computational approach was taken to study the promiscuity of the SAM(+)-dependent methyl transferase AtHTMT1 from thale cress with several nucleophiles (Cl-, Br-, I-, NCO-, NCS-). First, enzyme-free methyl transfer reactions were studied with M05/6-311+G(2d,p) DFT calculations and electrostatic continuum models (PCM/SMD) for various chemical environments. Second, QM/MM MD simulations with semiempirical Hamiltonians (PM7, PM6-D3, AM1, PM6-D3H4) and the AMBER 14SB force field were used to study the enzyme catalyzed reaction in silico. The combination of the DFT and MD results shows that reactant desolvation generally accelerates the reaction, but it cannot explain the selectivity of the enzyme. The critical position of H2O molecules at the reactive site favors the reaction of NCS- over Cl- and Br- in agreement with experiments, but not observed in the quantum calculations for the cytosol. The addition of selected H2O molecules to the N terminus of NCS- greatly increases its reactivity, while H2O molecules attached to Cl- slow the reaction. The partial solvation of the nucleophiles in the reactive pouch holds the key to understanding the reactivity of AtHTMT1.

Dative bonds between identical atoms of the same formal oxidation state are formed as geometric and electronic constraints turn an otherwise lone pair into a bond. Calculations at the B3LYP/6-31+g(d,p) level supported by additional atoms in molecules (AIM) and electron localization function (ELF) analyses on selected germanium polycations are used to prove the concept. The electron density (ρ) is not equally shared between the two atoms of such a homonuclear dative bond (HDB), and the associated charge transfer results in formal charges contradicting chemical convention.

The degradation of S-adenosyl methionine (SAM) to homoserine-γ-lactone (HSL) and methyltioadenine (MTA) in water is studied with MD simulations. The AM1 Hamiltonian is used for the quantum part and the flexible AMBER force field for the H2O molecules. The MD simulations predict the free energy barrier for the degradation reaction to be between 109 and 112 kJ mol-1 and an overall gain in free energy of -26 kJ mol-1. The high barrier and the low energy gain of this reaction can be linked to interactions among the carboxylate group of the SAM molecule and solvent H2O molecules, which are not observed on the product side. Hence, the H2O molecules effectively slow down the reaction that otherwise would be much faster.

A pseudo-enantiomeric pair of optically switchable helicenes containing a catalytic 4-N-methylaminopyridine (MAP) bottom unit and a C2-symmetric, (10R,11R)-dimethoxymethyl-dibenzosuberane top template was synthesized. They underwent complementary photoswitching at 290 nm (P/M', <1/>99) and 340 nm (P/M', 91/9) and unidirectional thermo-rotation at 130 °C (P/M', >99/<1). They were utilized to catalyze enantiodivergent Steglich rearrangement of O- to C-carboxylazlactones, with formation of either enantiomer with up to 91% ee (R) and 94% ee (S), respectively.

The Nicholas reaction is a proven and versatile tool in glycoside chemistry. Its application is less clear‐cut, if the intermediate Nicholas cation has two reactive sides that enable different reactions. Density functional theory (DFT) calculations are used to rationalize the observed difference in product yields for the Nicholas epimerization and substitution obtained from experiments with very similar glycosides. Substituents, which can increase the rigidity of the backbone, should be avoided in epimerization reactions as they can slow down reorientation of the intramolecular ion pair so that the substitution reaction dominates.

[2,3]-Wittig rearrangements of sugar-derived dihydropyran allyl propargyl ethers located at the 2- or 4-position have been studied as useful means for extending the carbon chains of the 4- or 2-position with chirality transfer. The stereochemical course of these reactions depends on the following factors: (1) deprotonation of pro-R or pro-S-H, (2) equilibration of the lithiated stereogenic carbanion, (3) conformational inversion during the rearrangement, and (4) concerted [2,3]- or [1,2]-Wittig rearrangement. In some cases, a stepwise mechanism that involves the allyl-C-O bond cleavage is shared as the first step by both the [2,3]- and [1,2]-Wittig rearrangements. The stereochemical courses of the rearrangements are compared among the lithiated reactants to determine the reaction pathways. These mechanisms in the polyoxygenated dihydropyran ring system were further supported by DFT calculations.

Quantum calculations show that βO4′ links break in two ways; the carbanion route yields monomers, the alkoxide route facilitates repolymerisation.

The formation of CH3Cl from (CH3)3SCl in various solvents has been studied based on M05/6-311+G(2d,p) DFT calculations to quantify the influence of the solvent on the stability of sulfonium cations. Four different pathways (one SN1, one backside and two frontside attacks for SN2) as well as the formation of different ion pairs (tripod, seesaw, and linear) are discussed to investigate the origin of the kinetic solvent effect (KSE) and the contribution of ion pairs to the overall reaction. Ion pairs are formed only in solvents with a permittivity ε lower than 28, but the reaction proceeds via a standard SN2 mechanism with a backside attack in all solvents. The formation of ion pairs does not change the order of the rate law, but it strongly influences the KSE, which can distinguish between reactions starting from free ions and those starting from ion pairs, in contrast to standard kinetic analysis.

Quantum calculations lead the way to a green version of the versatile Mannich reaction in water catalysed by nornicotine.

Allenoates and enones form cyclopentenes via a phosphine-catalyzed [3 + 2] cycloaddition while the amine-catalyzed [2 + 4] cycloaddition yields dihydropyrans or pyrans. The difference between these catalysts is studied with M06-2X/6-31+G* calculations. The addition of the catalyst to the allenoate is the first step in both pathways followed by the reaction with the enone. The formation of the [3 + 2] phosphorus-ylide is exergonic, and hence, the [3 + 2] cycloaddition is kinetically favored over the [2 + 4] addition. Amines do not stabilize [3 + 2] ammonium-ylides. However, electron-withdrawing groups on the enone enable [2 + 4] cycloadditions. The strength of the electron-withdrawing group further controls the α/γ regioselectivity of the [2 + 4] cycloaddition, and the analysis of the HOMO-LUMO interactions explains why only E-dihydropyrans from the direct γ-[2 + 4] cycloaddition have been observed in experiments. The quantum calculations further reveal a new path to the α-[2 + 4] product starting with an intermediate Rauhut-Currier reaction. This new path is kinetically favored over the direct amine-catalyzed α-[2 + 4] cycloaddition.

Several chemical properties of Lewis base-allenoate adducts (LB·allenoate), such as solvent effect, basicity, nucleophilicity and cycloaddition, are studied to provide a detailed foundation for the analysis of LB-catalyzed reactions of allenoates. The zwitterionic LB·allenoates formed between methyl allenoate and Lewis bases, such as N-heterocyclic carbenes (NHCs), phosphines, amines and aza-heterocycles, are studied at the M06-2X/6-31+G* level. The addition of the LBs to the allenoate can yield Z- or E-type adducts. The formation of the Z-type adducts is more favorable in the gas phase due to electrostatic interactions. The yield of the E-type adducts increases with the permittivity of the solvent. The lowest barriers for the addition and the most stable adducts are observed with NHCs as catalysts. It is also shown that the α-carbon atom of the allenic moiety in LB·allenoate is more nucleophilic than the γ-carbon atom. Aza-arenes, phosphines and NHCs stabilize the [3 + 2]-ylides formed by the cycloaddition of LB·allenoate to ethylene; therefore, these LBs thermodynamically support the [3 + 2] cycloadditions. The detailed analysis of [3 + 2]-, [2 + 4]-, [2 + 2]- and [2 + 2 + 2]-cycloadditions with enones/ketones shows that the amine-catalyzed reactions follow the kinetically preferred path, and that the exergonic formation of the P-ylide favors the [3 + 2] cycloaddition in the phosphine-catalyzed reaction. The thermodynamically preferred pathway is followed with NHCs whereas the high stability of NHC·allenoate adducts reduces the overall catalytic efficiency of NHCs.

A constrained reduced-dimensionality algorithm can be used to efficiently locate transition states and products in reactions involving conformational changes. The search path (SP) is constructed stepwise from linear combinations of a small set of manually chosen internal coordinates, namely the predictors. The majority of the internal coordinates, the correctors, are optimized at every step of the SP to minimize the total energy of the system so that the path becomes a minimum energy path connecting products and transition states with the reactants. Problems arise when the set of predictors needs to include weak coordinates, for example, dihedral angles, as well as strong ones such as bond distances. Two principal constraining methods for the weak coordinates are proposed to mend this situation: static and dynamic constraints. Dynamic constraints are automatically activated and revoked depending on the state of the weak coordinates among the predictors, while static ones require preset control factors and act permanently. All these methods enable the successful application (4 reactions are presented involving cyclohexane, alanine dipeptide, trimethylsulfonium chloride, and azafulvene) of the reduced dimensionality method to reactions where the reaction path covers large conformational changes in addition to the formation/breaking of chemical bonds. Dynamic constraints are found to be the most efficient method as they require neither additional information about the geometry of the transition state nor fine tuning of control parameters.

Density functional theory has been used to investigate the properties of organic high spin molecules. The M05/cc-pVDZ calculations predict a septet ground state for the 2,3,6,7,10,11-hexahydro-1,4,5,8,9,12-hexaoxocoronene-2,3,6,7,10,11-hexayl radical (coronene-6O). The computations show further that the formation of intermolecular carbon-carbon bonds yields a singlet ground state for the dimer rather than a possible tridectet state as expected from the monomer's multiplicity. A benzene molecule placed between coronene-6O molecules leads to the desired high-spin cluster, but the overall stability of the cluster is low. A chromium atom inserted between two peripheral C(6) rings of coronene-6O yields a sandwich structure with the expected tridectet ground state and a binding energy which is 15 times larger than the corresponding tridectet dimer stabilized by a benzene molecule. The presented DFT calculations suggest that a chromium atom can effectively link organic polyradicals to larger magnetic units.

The B3LYP/D95+(d,p) analysis of the uncharged low barrier hydrogen bond (LBHB) between 4-methyl-1H-imidazole (Mim) and acetic acid (HAc) shows that uncharged LBHBs can be formed either by adding three water molecules around the cluster or by placing the MimHAc pair in a dielectric environment created by a polarizable continuum model with a permittivity larger than 20.7. The permittivity of environment around uncharged LBHB can be lowered significantly by including water molecules into the system. A MimHAc LBHB stabilized with one water molecule observed in diethyl ether (e = 4.34), with two water molecules in toluene (e = 2.38), and with three water molecules in vacuo (e = 1). Solvation models with different numbers of water molecules predict average differences in the proton affinities of the hydrogen bonded bases (?PA) for stable uncharged LBHB systems in vacuo to be 91.5 kcal/mol being different from the ?PA values close to zero in charge-assisted LBHB systems. The results clearly indicate that small amounts of interstitial water molecules at the active site of enzymes do not preclude the existence of LBHBs in biological catalysis. Our results also show that interstitial water molecules provide a useful clue in the search for uncharged LBHBs in an enzymatic environment and the number of water molecules can be used as a relative measure for the polarity around the direct environment of LBHBs. (C) 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

Symplectin is a photoprotein containing the dehydrocoelenterazine (DCL) chromophore, which links to a cysteine residue through a covalent bond with the emission of blue light. This study focuses on the stereochemical process of the emerging stereogenic centers. Two isomeric fluorinated DCL analogs (2,4-diF- and 2,6-diF-DCL) were employed owing to their different bioluminescence activities, these being 200% and 20% compared to natural DCL, respectively. Each of these diF-DCLs was found to exchange with the natural DCL in symplectin at pH 6.0. The emerging stereogenic carbons were racemic at the binding sites. Changing the pH of this storage form to the protein's optimum solubility pH (pH 7.8) resulted in 2,4-diF-DCL-bound symplectin luminescence, and the spent solutions were then analyzed and coelenteramide-390-CGLK-peptide and coelenteramine were detected after a peptidase digestion. The same analysis of the 2,6-diF-DCL-bound symplectin, on the other hand, afforded coelenteramine only but no coelenteramide. When the racemic storage diF-DCLs moved to the active site at pH 7.8, a change in the chirality with the 390-Cys residue resulted. Model experiments using L-cysteine-containing CGLK-peptide supported two diastereoisomers from each diF-DCL. The significant difference in the luminescence from these two chromophores is attributed to a plausible mechanism including the dynamically variable stereogenic center emerging at the storage and then the active site on the symplectin. It is concluded that such dynamic chirality plays a significant role in the symplectoteuthis bioluminescence.

Density functional theory has been used to calculate the thermodynamic properties and molecular orbitals of pillar[n]quinones. Pillar[n]quinones are expected to be effective electron acceptors and the ability to accept more than one electron increases with the size of the interior cavity. Pillar[5]quinone and pillar[7]quinone show a great intramolecular charge transfer upon the electron excitation from highest occupied molecular orbital (HOMO) to lowest unoccupied molecular orbital (LUMO) as indicated by a large difference of electron distributions between their HOMO and LUMO and a notable dipole moment difference between the ground and first triplet excited state. The aggregation of pillar[n]quinones leads to tubular dimeric structures joined by 2n CH···O nonclassical hydrogen bonds (HBs) with binding energies about 2 kcal/mol per HB. The longitudinal extension of the supramolecular self‐assembly of pillar[n]quinone may be adjustable through forming and breaking their HBs by controlling the surrounding environment. The tunability of the diameter of the tubular structures can be achieved by changing the number of quinone units in the pillar[n]quinone. The electrostatic potential maps of pillar[n]quinones indicate that the positive charge in the interior cavity decreases as the number of quinone units increases. Chloride and bromide anions are chosen to examine the noncovalent anion‐π interactions between pillar[n]quinones and captured anions. The calculations show that the better compatibility of the effective radius of the anions with the interior dimension of pillar[n]quinone leads to larger stabilization energy. The selectivity of spatial matching and specific interaction of pillar[n]quinone is believed to possibly serve as a candidate for ionic and molecular recognition. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011

A series of model calculations was done to analyze the delocalization of the proton in the linking hydrogen bond of the (Dih)(2)H(+) cation (Dih: 4,5-dihydro-1H-imidazole). Standard quantum chemical calculations (B3LYP/D95+(d,p)) predict a low barrier hydrogen bond (LBHB) and thereby a delocalized proton in the NHN(+) hydrogen bridge. Explicit quantum calculations on the proton indicate that the delocalization of the proton does not provide enough energy to stabilize a permanent LBHB. Additional Born-Oppenheimer Molecular Dynamics (BOMD) simulations indicate further that the proton is localized at either side of the NHN(+) bridge and that a central proton position is the result of temporal averaging. The possibility of the proton to tunnel from one side to the other side of the NHN(+) bridge increases with the temperature as the trajectory of the (Dih)(2)H(+) cation runs through regions where the thermal excitation of Dih ring vibrations creates equal bonding opportunities for the proton on both sides of the bridge (vibrationally assisted proton tunneling). The quantum calculations for the proton in (Dih)(2)H(+) suggest further a broad peak for the 1 ← 0 transition with a maximum at 938 cm(-1) similar to that observed for LBHBs. Moreover, the asymmetric NHN(+) bridge in a thermally fluctuating environment is strong enough to create a significant peak at 1828 cm(-1) for the 2 ← 0 transition, while contributions from the 2 ← 1 are expected to be weak for the same reason.

The observation of the Asp–His–Ser triad (Asp: aspartate, His: histidine, Ser: serine) triad both in mammalian and bacterial proteases suggests a special efficiency. A series of B3LYP/D95*(d,p) calculations on various [X–H β Y] − dyads (as part of the [X–H β Y–H α Ac] − model triad, HAc: acetic acid) made from eight different anions X − and 15 different coupling elements H β Y was done to analyze the molecular origin of this efficiency. The X − anion acts merely as an electron density donor independent of its chemical nature, and the evolutionary selection of Asp for the catalytic triad therefore seems to be caused by the pH of the triads environment. As the linking proton H β moves from Y − to X − , electron density is effectively moved from X − to Y − thereby increasing the proton affinity (PA) of the [X–HY] − dyad, which finally leads to the deprotonization of the HAc molecule. The degree to which the position of H α controls the PA is dominatly determined by the coupling element HY. The model calculations indicate that 4‐methyl‐1 H ‐imidazole (HMim) is a very efficient coupling element, which suggest that the evolutionary convergence to the Asp–His–Ser is not only controlled by the ready availability of the imidazole motive in His but also by its high efficiency. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010