Mechanisms in the Synthesis of S-Alcohols with 1,4-NADH Biomimetic Co-factor N-Benzyl-1,4-dihydronicotinamide using Horse Liver Alcohol Dehydrogenase: A Hybrid Computational Study.

The enantioselective reduction of prochiral ketones catalyzed by horse liver alcohol dehydrogenase (HLADH), was investigated via a hybrid computational approach, for molecular reactions involved in chiral synthesis of S-alcohols, when the natural co-factor, 1,4-dihyronicotinamide adenine dinucleotide, 1,4-NADH, was replaced with biomimetic co-factor, N-benzyl-1,4-dihydronicotinamide, 1.  We surmised that different hydride and proton transfer mechanisms were involved using co-factor, 1. An alternative mechanism, where the hydride transfer step occurred, via an η1-keto-S-η2-5,6-1,4-dihydronicotinamide-Zn(II) complex, was previously investigated with a model of the HLADH-Zn(II) catalytic site (J. Organometal. Chem. 2021, 943, 121810).  Presently, we studied canonical and alternative mechanisms compared to models of the entire enzyme structure.  We disproved the η2-Zn(II) complex, and discovered a canonical hydride transfer from biomimetic 1,4-NADH, 1, to the Zn(II) bound prochiral ketone substrate, followed by a new proton relay, consisting of a water chain connecting His51 to Ser48 that accomplished the S-alkoxy anion's protonation to yield the final S-alcohol product. The HLADH catalysis, with biomimetic co-factor, 1, that replaced the ribose group, the 5'-diphosphate groups, and the adenine nucleotide with a N-benzyl group, has provided a new paradigm for the design of other structures of 1,4-NADH biomimetic co-factors, including their economic value in biocatalysis reactions.

Room-Temperature Single-Molecule Infrared Imaging and Spectroscopy through Bond-Selective Fluorescence.

Infrared (IR) spectroscopy stands as a workhorse for exploring bond vibrations, offering a wealth of chemical insights across diverse frontiers. With increasing focus on the regime of single molecules, obtaining IR-sensitive information from individual molecules at room temperature would provide essential information about unknown molecular properties. Here, we leverage bond-selective fluorescence microscopy, facilitated by narrowband picosecond mid-IR and near-IR double-resonance excitation, for high-throughput mid-IR structural probing of single molecules. We robustly capture single-molecule images and analyze the combined polarization dependence, vibrational peaks, linewidths, and lifetimes of probe molecules with representative scaffolds. From bulk to single molecules, we find that vibrational lifetimes remain consistent, while linewidths are narrowed by approximately twofold and anisotropy becomes more pronounced. Additionally, unexpected peak shifts from single molecules were observed, attributed to the generation of new modes due to previously unexplored dimerization, supported by quantum chemistry calculations. These findings underscore the importance of infrared analysis on individual single molecules in ambient environments, offering molecular information crucial for functional imaging and the investigation of the fundamental properties and utilities of luminescent molecules.

Codoped germanene with 3p and 4p elements elements.

CONTEXT: The relentless need for new materials to be used in electronic devices has opened new research directions in materials science. One of them involves using two-dimensional materials, among which there is current interest in using germanene. The heteroatom doping of germanene has been proposed as a possible approach to fine-tuning its electronic properties. However, this procedure is complicated because locating the dopants with a specific arrangement is challenging, thus achieving reproducibility. To avoid this problem, we propose the codoping of germanene to understand if dopants prefer to be agglomerated as observed for graphene or if they prefer to adopt a random disposition. Herein, we employed first-principles calculations to study 21 codoped germanene systems with one 3p (Al, Si, P, and S) and one 4p (Ga, As, and Se) element. Our results indicate that in the cases of AlP, AlS, GaP, GaS, GaAs, and GaSe codoped germanene, the dopants show a tendency to be located in specific lattice positions. The ortho disposition of dopants is preferred for AlP, AlS, GaP and GaS codoped germanene and their 4p counterparts GaAs and GaSe codoped germanene, and the materials showed interesting electronic properties making them suitable to develop germanene-based electronic materials. METHODS: We utilized the M06-L, HSE06 methods accompanied by the 6-31G* basis sets to perform periodic boundary conditions calculations as implemented in Gaussian 09. The unit cells were sampled employing 100 k-points for geometry optimizations and 2000 k-points for electronic properties The ultrafine grid was employed. Results were visualized employing Gaussview 5.0.1. In addition to this, we performed B3LYP-D3 periodic calculations as implemented in CRYSTAL17.

Illuminating the Performance of Electron Withdrawing Groups in Halogen Bonding.

Throughout the halogen bonding literature, electron withdrawing groups are relied upon heavily for tuning the in- teraction strength between the halogen bond donor and acceptor; however, the interplay of electronic effects associated with various substituents is less of a focus. This work utilizes computational techniques to study the degree of σ- and π- electron donating/accepting character of electron withdrawing groups in a prescribed set of halo-alkyne, halo-benzene, and halo-ethynyl benzene halogen bond donors. We examine how these factors affect the σ-hole magnitude of the donors as well as the binding strength of the corresponding complexes with an ammonia acceptor. Statistical analyses aid the interpretation of how these substituents influence the properties of the halogen bond donors and complexes, and show that the electron withdrawing groups that are both σ- and π-electron accepting form the strongest halogen bond complexes.

Confinement Effects of Two-dimensional Surfaces on Water Adsorption and Dissociation over Pt(111).

It has been established that the  confined space created by stacking a two dimensional (2D) surface atop a metal catalyst serves as a nano-reactor. According to recent research, when a graphene (Gr) overlayer encloses a Pt catalyst from above, the activation barrier for the water dissociation reaction, a process with major industrial significance, decreases. In order to investigate how the effect of confinement varies among different two-dimensional (2D) materials, we study the adsorption and dissociation barriers of water molecule on Pt(111) under graphene, hexagonal boron nitride (h-BN), and heptazine-based graphitic carbon nitride (g-C3N4) layers using density functional theory calculations. Our findings reveal that the strength of adsorption does not decrease consistently with a reduction in the height of the 2D overlayer. Furthermore, a smaller barrier is not always the consequence of poorer adsorption of the reactant. We also examine the effect of confinement on the shape of the reaction path, on the frequencies of vibrational modes, and on the rate constants derived using the harmonic transition state theory. Overall, all three of the 2D surfaces cause a decrease in barrier height and a weakening of adsorption, though to differing degrees due to a mix of mechanical, geometric and electronic variables.

Multiple pathways for lanthanide sensitization in self-assembled aqueous complexes.

Lanthanide photoluminescence (PL) emission has attracted much attention for technological and bioimaging applications because of its particularly interesting features, such as narrow emission bands and very long PL lifetimes. However, this emission process necessitates a preceding step of energy transfer from suitable antennas. While biocompatible applications require luminophores that are stable in aqueous media, most lanthanide-based emitters are quenched by water molecules. Previously, we described a small luminophore, 8-methoxy-2-oxo-1,2,4,5-tetrahydrocyclopenta[de]quinoline-3-phosphonic acid (PAnt), which is capable of dynamically coordinating with Tb(III) and Eu(III), and its exchangeable behavior improved their performance in PL lifetime imaging microscopy (PLIM) compared with conventional lanthanide cryptate imaging agents. Herein, we report an in-depth photophysical and time-dependent density functional theory (TD-DFT) computational study that reveals different sensitization mechanisms for Eu(III) and Tb(III) in stable complexes formed in water. Understanding this unique behavior in aqueous media enables the exploration of different applications in bioimaging or novel emitting materials.

Computational study on the Maillard reactions of glucose and galactose with lysine.

CONTEXT: Milk has nutrient-rich but thermal sensitive matrix that undergoes varying degrees of Maillard reaction (MR) at heating conditions. The MR mainly occurs between lysine residues (Lys) and lactose composed of glucose (Glc) and galactose (Gal), which are abundantly sourced from dairy products. In the present study, the MRs of Glc and Gal with Lys at the initial and intermediate stages have been investigated theoretically using density functional theory (DFT) to simulate the gaseous and aqueous phases. Reaction mechanisms have been proposed, and relative energy changes of different steps were calculated according to the total mass balance. The calculations reveal that both Nα- and Nε-amine groups of Lys can react with the carbonyl functional group of Glc and Gal with the similar potential energy profiles, and Gal is more reactive than Glc. However, the barrier in Nε-channel is lower than in Nα-channel, indicating a faster reaction rate through the former channel compared with the latter. The 5-hydroxymethyl-2-furfural (HMF) and derivative are formed under 3-deoxysone route in the intermediate stage. The calculation results are helpful for proposing a reasonable MR mechanism and suggesting possible control methods of the MRs. METHODS: In this study, different levels of DFT calculations have been conducted to investigate the mechanisms and favorability of generating MR products in Glc-Lys and Gal-Lys models at initial and intermediate stages in the gaseous and aqueous conditions. In order to elucidate the molecular models from the perspectives of chemistry and geometry, DFT calculations were performed by the mean of B3LYP functional at basis sets of 6-311 + + G (d, p) and 6-311 + + G (2df, 2p) with optional solvation settings. To examine the solvation effect, the study further constructed models with solvent H2O and calculated in wB97XD functional with 6-31 + G (d) basis set. All computations were carried out Gaussian 09 suite of quantum chemistry software.

Peripheral Fusion of Carbon-based Aromatic Rings to B4N4-Heteropentalene Leading to Close π-Stacking in the Solid State.

π-Electronic molecules with a BN-heterocyclic and carbon-based aromatic hybrid ring system (h-CBN) are interesting in that they potentially exhibit synergistic properties arising from the two different π-systems. Here we report the synthesis and properties of a h-CBN-type molecule (1) having a bicyclic B4N4-heteropentalene core fused with extended aromatic rings. This molecule exhibits excellent chemical stability despite the absence of bulky substituents for kinetic protection, which in turn provides effective stacking of the π-system upon crystallization. Depending on the crystallization solvent, 1 forms two polymorphs, i.e., the α- and ß-phases. While both phases have one-dimensional columnar structures, the π-stacking geometries associated with the transfer integrals of the frontier orbitals are different, resulting in a twofold difference in the electrical conducting properties. We also found that upon thermal vacuum deposition, 1 gives an amorphous film, which serves as a host material for a red phosphorescent OLED device (maximum external quantum efficiency: 15.5 and 13.3% at 0.1 and 2.5 mA, respectively).

A Computational Study of Reactions with Boric Acid Aimed to Promote the Utilization of Lignin.

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.

The Dialuminene AriPr8AlAlAriPr8 (AriPr8 = C6H-2,6-(C6H2-2,4,6-iPr3)2-3,5-iPr2).

Careful analysis of the crystals formed in the reduction of AriPr8AlI2 (AriPr8 = C6H-2,6-(C6H2-2,4,6-iPr3)2-3,5-iPr2) with sodium on sodium chloride showed them to contain the long sought-after dialuminene AriPr8AlAlAriPr8 (1) that forms alongside the previously characterized alanediyl:AlAriPr8. The single crystal X-ray structure of 1 revealed a nearly planar, trans-bent C(ipso)AlAlC(ipso) core with an Al-Al distance of 2.648(2) Å. The molecular and electronic structure of 1 are consistent with a Al-Al double dative interaction augmented with diradical character and stabilized by dispersion interactions. Density functional theory calculations showed that the reactivity of:AlAriPr8 with dihydrogen involves 1, not:AlAriPr8, as the reactive species. In contrast, the reaction of:AlAriPr8 with ethylene gave two products, the 1,4-dialuminacyclohexane AriPr8Al(C2H4)2AlAriPr8 (2) and the aluminacyclopentane AriPr8Al(C4H8) (3), that can both form from the aluminacyclopropane intermediate AriPr8Al(C2H4). Although the [2+2+2] cycloaddition of 1 with two equivalents of ethylene was also calculated to be exergonic, it is likely to be kinetically blocked by the numerous isopropyl substituents surrounding the Al-Al bond. Attempts to fine-tune the steric bulk of the terphenyl ligand to allow stronger Al-Al bonding were unsuccessful, leading to the isolation of the sodium salt of a cyclotrialuminene, Na2[AlAriPr6]3 (4), instead of AriPr6AlAlAriPr6.

Selective Chromogenic Chemosensors for Arsenite Anion: A Facile Approach to Analyzing Arsenite in Honey, Milk, and Water samples.

In this study, two chemosensors, N5R1 and N5R2, based on 5-(4-nitrophenyl)-2-furaldehyde, with varying electron-withdrawing groups, were synthesized and effectively employed for the colorimetric selective detection of arsenite anions in a DMSO/H2O solvent mixture (8:2, v/v). Chemosensors N5R1 and N5R2 exhibited a distinct color change upon binding with arsenite, accompanied by a spectral shift toward the near-infrared region (Δλmax exceeding 200 nm). These chemosensors established stability between a pH range 6-12. Among them, N5R2 displayed the lowest detection limit of 17.63 ppb with a high binding constant of 2.6163×105 M⁻1 for arsenite. The binding mechanism involved initial hydrogen bonding between the NH binding site and the arsenite anion, followed by deprotonation and an intramolecular charge transfer (ICT) mechanism. The mechanism was confirmed through UV and 1H NMR titrations, cyclic voltammetric studies, and theoretical calculations. The interactions between the sensor and arsenite anions were further analyzed using global reactivity parameters (GRPs). Practical applications were demonstrated through the utilization of test strips and molecular logic gates. Real water samples, honey, and milk samples were successfully analyzed by both chemosensors for the sensing of arsenite.

Chemical Orderings in CuCo Nanoparticles: Topological Modeling Using DFT Calculations.

The orderings of atoms in bimetallic 1.6-2.1 nm-large CuCo nanoparticles, important as catalytic and magnetic materials, were studied using a combination of DFT calculations with a topological approach. The structure and magnetism of Cu50Co151, Cu101Co100, Cu151Co50, and Cu303Co102 nanoparticles; their resistance to disintegrating into separate Cu and Co species; as well as the exposed surface sites, were quantified and analyzed, showing a clear preference for Cu atoms to occupy surface positions while the Co atoms tended to form a compact cluster in the interior of the nanoparticles. The surface segregation of Co atoms that are encapsulated by less-active Cu atoms, induced by the adsorption of CO molecules, was already enabled at a low coverage of adsorbed CO, providing the energy required to displace the entire compact Co species inside the Cu matrices due to a notable adsorption preference of CO for the Co sites over the Cu ones. The calculated adsorption energies and vibrational frequencies of adsorbed CO should be helpful indicators for experimentally monitoring the nature of the surface sites of CuCo nanoparticles, especially in the case of active Co surface sites emerging in the presence of CO.

Ring Contraction of Saturated Cyclic Amines and Rearrangement of Acyclic Amines Through Their Corresponding Hydroxylamines.

Compared to modifications at the molecular periphery, skeletal adjustments present greater challenges. Within this context, skeletal rearrangement technology stands out for its significant advantages in rapidly achieving structural diversity. Yet, the development of this technology for ring contraction of saturated cyclic amines remains exceedingly rare. While most existing methods rely on specific substitution patterns to achieve ring contraction, there is a persistent demand for a more general strategy for substitution-free cyclic amines. To address this issue, we report a B(C6F5)3-catalyzed skeletal rearrangement of hydroxylamines with hydrosilanes. This methodology, when combined with the N-hydroxylation of amines, enables the regioselective ring contraction of cyclic amines and proves equally effective for rapid reorganization of acyclic amine skeletons. By this, the direct scaffold hopping of drug molecules and the strategic deletion of carbon atoms are achieved in a mild manner. Based on mechanistic experiments and density functional theory calculations, a possible mechanism for this process is proposed.

High Rotational Barrier Atropisomers.

Atropisomers have attracted a great deal of attention lately due to their numerous applications in organic synthesis and to their employment in drug discovery. However, the synthetic arsenal at our disposal with which to access them remains limited. The research described herein is two-pronged; we both demonstrate the use of MCR chemistry as a synthetic strategy for the de novo synthesis of a class of atropisomers having high barriers to rotation with the simultaneous insertion of multiple chiral elements and we study these unprecedented molecular systems by employing a combination of crystallography, NMR and DFT calculations. By fully exploiting the synthetic capabilities of our chemistry, we have been able to monitor a range of different types of interaction, i. e. π-π, CH-π, heteroatom-π and CD-π, in order to conduct structure-property studies. The results could be applied both to atroposelective synthesis and in drug discovery.

Aluminum Alkyl Induced Isomerization of Group†IV meso Metallocene Complexes.

The synthesis of group IV metallocene precatalysts for the polymerization of propylene generally yields two different isomers: The racemic isomer that produces isotactic polypropylene (iPP) and the meso isomer that produces atactic polypropylene (aPP). Due to its poor physical properties, aPP has very limited applications. To avoid obtaining blends of both polymers and thus diminish the mechanical and thermal properties of iPP, the meso metallocene complexes need to be separated from the racemic ones tediously-rendering the metallocene-based polymerization of propylene industrially far less attractive than the Ziegler/Natta process. To overcome this issue, we established an isomerization protocol to convert meso metallocene complexes into their racemic counterparts. This protocol increased the yield of iPP by 400 % while maintaining the polymer's excellent physical properties and was applicable to both hafnocene and zirconocene complexes, as well as different precatalyst activation methods. Through targeted variation of the ligand frameworks, methoxy groups at the indenyl moieties were found to be the structural motifs responsible for an isomerization to take place-this experimental evidence was confirmed by density functional theory calculations. Liquid injection field desorption ionization mass spectrometry, as well as 1H and 29Si nuclear magnetic resonance studies, allowed the proposal of an isomerization mechanism.

A Data-Driven Approach for Enhanced CO2 Capture with Ruthenium Complexes.

To attain carbon neutrality, significant efforts have been made to capture and utilize CO2. The homogeneous hydrogenation of CO2 catalyzed by transition metal complexes, particularly the ruthenium complexes, has demonstrated significant advantages and is regarded as a viable approach for practical application. Insertion of CO2 into the Ru-H bond, producing the Ru-formate product, is the key step in the hydrogenation of CO2. In order to parameterize the catalytic activities in the CO2 insertion into the Ru-H bond, the concept of simplified mechanism-based approach with data-driven practice (SMADP) has been introduced in this paper. The results showed that the hydricity of the Ru-H complex (ΔGH-) might serve as a single active descriptor in the process of CO2 insertion, and that a novel ruthenium complex in CO2 catalysis may not be easily obtained by mere modification of the auxiliary ligand at the ruthenium metal site.

Investigating the Mechanism of Triboluminescence: Insights from Structural and Electrostatic Characterization of Copper Thiocyanate Complexes.

Triboluminescence is a phenomenon in which light is generated through mechanical stress; it has emerging applications in stress-sensing devices. Although the prevailing mechanistic model indicates that light emits from charge separation and recombination in fracture planes arising from polar structures, its application in designing triboluminescent materials remains limited owing to numerous exceptions. This study provides insights into the essential requirements for triboluminescence by investigating the structural and electrostatic properties of fractured crystals of copper thiocyanate complexes. The examined fracture plane indicated that charge pairs (which are essential for light emission) form when intermolecular interactions are disrupted during fracturing. On the basis of the nature of these charges, we successfully suppressed triboluminescence by inhibiting the formation of intermolecular interactions disrupted in the examined complexes. Furthermore, we induced its re-emergence by creating an alternative fracture plane through controlled manipulation of the molecular network. This demonstrative deactivation and reactivation of triboluminescence underscores the critical role of intermolecular disruption in generating charge pairs, a prerequisite for triboluminescence.

Origins of Temperature-Dependent Anomeric Selectivity in Glycosylations with an L-Idose Thioglycoside.

L-Idose thioglycosides are useful glycosyl donors for the construction of glycosaminoglycan oligosaccharides. When activated with NIS and catalytic TMSOTf in the presence of methanol, the stereoselectivity of O-glycosylation displays an intriguing dependence on the reaction temperature, with an increased preference for formation of the α-glycoside at higher temperatures. Using a combination of vt-NMR spectroscopy and DFT calculations, we show how a simple mechanistic model, based on competing reactions of the iodinated thioglycoside, can explain the main features of the temperature dependence. In this model, the increased selectivity at high temperature is attributed to differences among the entropy and energy terms of the competing reaction pathways. Neighbouring-group participation (giving an intermediate acyloxonium ion) plays an increasingly dominant role as temperature is raised. The general features of this kinetic regime may also apply more broadly to other glycosylations that likewise favour α-glycoside formation at high temperature.

Cationic Bis(hydrosilane)-Coinage-Metal Complexes: Synthesis, Characterization, and Use as Catalysts for Outer-Sphere C=O Hydrosilylation Not Involving Metal Hydrides.

The preparation of cationic bis(hydrosilane)-coinage-metal complexes by chloride abstraction from the neutral metal chloride precursors with Na[BArF 4] is described. Unlike previously reported hydrosilane-stabilized copper and silver complexes, the presented complexes are cationic and feature two bidentate (ortho-silylphenyl)phosphine ligands. These complexes were fully characterized by NMR spectroscopy and X-ray diffraction analysis, revealing that both Si-H bonds are activated by the Lewis acidic cationic metal center. The new complexes were found to be effective in catalytic carbonyl hydrosilylation, leading to the corresponding silyl ethers under mild conditions without the addition of an external base. Combined mechanistic control experiments and quantum chemical calculations support an ionic outer-sphere mechanism, in which a neutral metal alkoxide species instead of a metal hydride is the key intermediate that interacts with the silylcarboxonium ion to generate the silyl ether.

Au⋠⋠⋠H-X (X=N or C) Intramolecular Interactions in Gold (I)-NHC Carbene Complexes with Potential Anticancer Properties: A Quantum Mechanical Study with Two Basis Sets.

Three cationic Gold(I)-NHC complexes with potential anticancer properties were studied using DFT with B3LYP functional in combination with two basis sets, LanL2DZ and SDD. Obtained equilibrium geometries and computed IR spectra were found in excellent agreement with previously reported x-ray structures and experimental IR spectral data. NBO population analysis showed gold(I) has a charge deficiency of 0.26-0.30 e. All three complex cations are polar, with dipole moment values ranging from 6.8 to 7.4 Debye. Regardless of some structural differences in their co-ligands, all three complex cations have remarkably similar HOMO-LUMO energy gaps, with values ranging from 5.2 to 5.4 eV, confirming they are chemically stable and that they share an almost identical stability. Long-range intramolecular interactions Au ⋅⋅⋅H-X (X=N or C) in all three cationic complexes were identified. Both basis sets employed in this study were found equally effective in producing reliable results.