NCIPLOT: a program for plotting non-covalent interaction regions

Key-to-lock halogen bond-based tetragonal pyramidal association of iodonium cations with the lacune rims of beta-octamolybdate

The structure-directing "key-to-lock" interaction of double σ-(IIII)-hole donating iodonium cations with the O-flanked pseudo-lacune rims of [β-Mo8O26]4- gives halogen-bonded iodonium-beta-octamolybate supramolecular associates. In the occurrence of their tetragonal pyramidal motifs, deep and broad σ-(IIII)-holes of a cation recognize the molybdate backbone, which provides an electronic pool localized around the two lacunae. The halogen-bonded I⋯O linkages in the structures were thoroughly studied computationally and classified as two-center, three-center bifurcated, and unconventional "orthogonal" I⋯O halogen bonds. In the latter, the O-atom approaches orthogonally the C-IIII-C plane of an iodonium cation and this geometry diverge from the IUPAC criteria for the identification of the halogen bond.

Degradation of Di (2-ethylhexyl) phthalic acid plasticizer in baijiu by a foam titanium flow reactor attached with hairpin-like structured peptide enzyme mimics

Because of the significant environmental and health hazards imposed by di(2-ethylhexyl) phthalate (DEHP), a common plasticizer, developing safe and green techniques to degrade DEHP plasticizer is of huge scientific significance. It has been observed that environmental contamination of DEHP may also induce serious food safety problems because crops raised in plasticizers contaminated soils would transfer the plasticizer into foods, such as Baijiu. Additionally, when plastic packaging or vessels are used during Baijiu fermentation and processing, plasticizer compounds frequently migrate and contaminate the product. In this study, hairpin-like structured peptides with catalytically active sites containing serine, histidine and aspartic acid were found to degrade DEHP. Furthermore, after incorporating caffeic acid molecules at the N-terminus, the peptides could be attached onto foam titanium (Ti) surfaces via enediol-metal interactions to create an enzyme-mimicking flow reactor for the degradation of DEHP in Baijiu. The structure and catalytic activity of peptides, their interaction with DEHP substrate and the hydrolysis mechanism of DEHP were discussed in this work. The stability and reusability of the peptide-modified foam Ti flow reactor were also investigated. This approach provides an effective technique for the degradation of plasticizer compounds.

Impact of the Acetyl Group on Cysteine: A Study of N-Acetyl-Cysteine through Rotational Spectroscopy

Herein, we report a spectroscopic study of N-acetyl-L-cysteine, an important antioxidant drug, using Fourier-transform microwave techniques and in isolated conditions. Two conformers are observed, where most stable structure adopts a cis disposition, and the second conformer has a lower abundance and adopts a trans disposition. The rotational constants and the barriers to methyl internal rotation are determined for each conformer, allowing a precise conformation identification. The results show that the cis form adopts an identical structure in the crystal, solution, and gas phases. Additionally, the structures are contrasted against those of cysteine.

Current developments and trends in quantum crystallography

Quantum crystallography is an emerging research field of science that has its origin in the early days of quantum physics and modern crystallography when it was almost immediately envisaged that X-ray radiation could be somehow exploited to determine the electron distribution of atoms and molecules. Today it can be seen as a composite research area at the intersection of crystallography, quantum chemistry, solid-state physics, applied mathematics and computer science, with the goal of investigating quantum problems, phenomena and features of the crystalline state. In this article, the state-of-the-art of quantum crystallography will be described by presenting developments and applications of novel techniques that have been introduced in the last 15 years. The focus will be on advances in the framework of multipole model strategies, wavefunction-/density matrix-based approaches and quantum chemical topological techniques. Finally, possible future improvements and expansions in the field will be discussed, also considering new emerging experimental and computational technologies.

Diphenylene Iodonium as a Prominent Halogen Bond Donor: The Case of Human Monoamine Oxidase B

Herein we have investigated the formation and interplay of several noncovalent interactions (NCIs) involved in the inhibition of human monoamine oxidase B (MAO B). Concretely, an inspection of the Protein Data Bank (PDB) revealed the formation of a halogen bond (HlgB) between a diphenylene iodonium (DPI) inhibitor and a water molecule present in the active site, in addition to a noncovalent network of interactions (e. g. lone pair-π, hydrogen bonding, OH-π, CH-π and π-stacking interactions) with surrounding protein residues. Several theoretical models were built to understand the strength and directionality features of the HlgB in addition to the interplay with other NCIs present in the active site of the enzyme. Besides, a computational study was carried out using DPI as HlgB donor and several electron rich molecules (CO, H2O, CH2O, HCN, pyridine, OCN-, SCN-, Cl- and Br-) as HlgB acceptors. The results were analyzed using several state-of-the-art computational tools. We expect that our results will be useful for those scientists working in the fields of rational drug design, chemical biology as well as supramolecular chemistry.

Co-regulating the pore structure and surface chemistry of sludge-based biochar for high-performance deodorization of gaseous dimethyl disulfide

A straightforward and eco-friendly preparation method for porous sludge biochar (SBA-3) was developed to deodorize gaseous dimethyl disulfide (DMDS) using ion exchange to adjust micropore structures coupled with carboxyl functionalization. Compared with the unmodified sludge biochar SBA-1 and SBA-2 treated with ion exchange, the pore size of SBA-3 decreased accompanied with increasing specific surface area and micropore volume. The Brunauer-Emmett-Teller (BET) specific surface area and micropore volume were 176.35 and 0.0314 cm³ g-1, which were 2.02 and 1.71-fold larger than those of SBA-2, as well as 20.60 and 78.5-fold larger than those of SBA-1, respectively. Meanwhile, the amount of -COOH on the surface of SBA-3 increased from 0.425 to 1.123 mmol g-1, which was 2.64-fold larger than that of SBA-1. The adsorption behavior between DMDS and SBA-3 could be well described by the quasi-second-order kinetic model and Langmuir isotherm model. The maximum monolayer adsorption capacity was 35.12 mg g-1 at 303 K. Thermodynamic and DFT calculations indicated that the adsorption of DMDS on SBA-3 was exothermic with the deodorization mechanisms involving pore filling and chemisorption.

Multi-component Crystal Strategy for Improving Water Solubility and Antifungal Activity of Climbazole

PURPOSE

The primary problem with climbazole (CLB), a broad-spectrum imidazole antifungal drug, is its low water solubility. In order to increase its water solubility and antifungal activity, three new multi-component crystals were synthesized in this work, and the intermolecular interactions were systematically studied. This work helps to optimize the CLB product formulation and extend its application prospects.

METHODS

In this work, three novel multi-component crystals, CLB-malonic acid (CLB-MA) salt, CLB-succinic acid (CLB-SA) cocrystal and CLB-adipic acid (CLB-AA) cocrystal, were successfully synthesized. And the crystal structure, thermodynamic properties, solubility, dissolution, hygroscopicity, and antifungal activity of the three multi-component crystals were fully characterized by single-crystal X-ray diffraction (SCXRD), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), dynamic water vapor adsorption (DVS) and powder dissolution tests, etc. The molecular interactions and molecular stacking in multi-component crystals were studied by Hirshfeld surface (HS), molecular surface electrostatic potential (MEP), interaction region indication (IRI) and atom and molecule (AIM) techniques.

RESULTS

The results show that the three multi-component crystals have good moisture resistance stability, and their water solubility is 6-22 times that of pure CLB. Meanwhile, the measurement of the minimum inhibitory concentration (MIC) proves that the cocrystal/salt has a stronger antifungal activity than climbazole. Quantum chemistry calculations of crystal structure visualized and quantified the interactions that exist in multi-component crystals, and explored the microscopic mechanisms underlying the different performance of multi-component crystals.

Theoretical Study of Structural and Electronic Trends of the Sulfonylurea Herbicides Family

The sulfonylurea herbicide family has been extensively studied using computational techniques. The most stable conformer structures of the 34 molecules analyzed in gaseous, aqueous, and octanol phases have been determined. The study employed CREST conformational search methods along with the CENSO script to explore all possible conformational structures. Additional evaluations conducted at the B3LYP-D3/6-311+G(d,p) level have enabled the identification of intramolecular stability patterns across the various compounds. It has been discovered that stability is primarily determined by two factors: intramolecular hydrogen bonding involving an NH group adjacent to the sulfonyl group with either N donors or the nearby carbonyl group and potential π-π interactions between the aromatic rings of the molecules. These have been characterized through QTAIM and NCI population analyses. Furthermore, with the goal of developing predictive models for the physicochemical properties of pesticides that include the sulfonylurea family, a statistical analysis among the different properties of the studied molecules has been conducted. Significant correlations have been found between various properties, predicting a promising future for the prediction of characteristics that could assist laboratories in selecting among different pesticides.

Microwave spectroscopic and computational analyses of the phenylacetylene⋯methanol complex: insights into intermolecular interactions

The microwave spectra of five isotopologues of phenylacetylene⋯methanol complex, C6H5CCH⋯CH3OH, C6H5CCH⋯CH3OD, C6H5CCH⋯CD3OD, C6H5CCD⋯CH3OH and C6H5CCH⋯13CH3OH, have been observed through Fourier transform microwave spectroscopy. Rotational spectra unambiguously unveil a specific structural arrangement characterised by dual interactions between the phenylacetylene and methanol. CH3OH serves as a hydrogen bond donor to the acetylenic π-cloud while concurrently accepting a hydrogen bond from the ortho C-H group of the PhAc moiety. The fitted rotational constants align closely with the structural configuration computed at the B3LYP-D3/aug-cc-pVDZ level of theory. The transitions of all isotopologues exhibit doublets owing to the methyl group's internal rotation within the methanol molecule. Comprehensive computational analyses, including natural bond orbital (NBO) analysis, atoms in molecules (AIM) theory, and non-covalent interactions (NCI) index plots, reveal the coexistence of both O-H⋯π and C-H⋯O hydrogen bonds within the complex. Symmetry adapted perturbation theory with density functional theory (SAPT-DFT) calculations performed on the experimentally determined geometry provide an insight into the prominent role of electrostatic interactions in stabilising the overall structural arrangement.

Fragment Aligned Molecular Orbital Analysis: An Innovative Tool for Analyzing Atypical Chemical Bonding

In chemical research, it is a common practice to carry out quantum chemical calculations and analyze the canonical molecular orbitals (CMOs) obtained to study electronic structures of chemical systems. However, extensive orbital mixing of CMOs especially in molecular clusters significantly complicates our understanding of the electronic structures. In this paper, we have developed an innovative tool called fragment aligned molecular orbital (FAMO) analysis, which reconstructs our modular chemical picture by making use of the Procrustes analysis in statistical theory to align the occupied molecular orbitals of a molecular species against the occupied (molecular) orbitals of the constituting fragments of the cluster, and results in a set of chemically intuitive semilocalized orbitals. This alignment technique minimizes the extensive orbital mixing, thus allowing precise observation of bonding interactions in complex chemical systems. A few representative clusters have been selected as showcase examples to demonstrate the advantage of FAMO analysis in deciphering the distinct bonding interactions in cluster compounds.

Self-healable, stimuli-responsive bio-ionic liquid and sodium alginate conjugated hydrogel with tunable Injectability and mechanical properties for the treatment of breast cancer

Designing stimuli-responsive drug delivery vehicles with higher drug loading capacity, sustained and targeted release of anti-cancer drugs and able to mitigate the shortcomings of traditional systems is need of hour. Herein, we designed stimuli-responsive, self-healable, and adhesive hydrogel through synergetic interaction between [Cho][Gly] (Choline-Glycine) and sodium alginate (SA). The hydrogel was formed as a result of non-covalent interaction between the components of the mixture forming the fibre kind morphology; confirmed through FTIR/computational analysis and SEM/AFM images. The hydrogel exhibited excellent mechanical strength, self-healing ability, adhesive character and most importantly; adjustable injectability. In vitro biocompatibility of the hydrogel was tested on HaCaT and MCF-7 cells, showing >92 % cell viability after 48 h. The hemolysis ratio (<4 %) of the hydrogel confirmed the blood compatibility of the hydrogel. When tested for drug-loading capacity, the hydrogel show 1500 times drug loading for the 5-fluorouracil (5-FU) against the SA based hydrogel. In vitro release data indicated that 5-FU have more preference towards the cancerous cell condition, i.e. acidic pH (>85 %), whereas the drug-loaded hydrogel successfully killed the MCF-7 and HeLa cell with a Collapse

Key Words

• Bio-ionic liquid
• Injectable-hydrogel
• Sodium alginate

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Affiliation(s)

Raviraj Pansuriya Ionic Liquids Research Laboratory, Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat 395007, Gujarat, India
Tapas Patel Ionic Liquids Research Laboratory, Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat 395007, Gujarat, India
Kuldeep Singh Salt and Marine Chemicals Division, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific and Industrial Research, G. B. Marg, Bhavnagar 364002, India
Azza Al Ghamdi Department of Chemistry, College of Science, Imam Abdul Rahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia; Basic & Applied Scientific Research Center (BASRC), Water Treatment Unit, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
Naresh Kasoju Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum 695011, Kerala, India
Arvind Kumar Salt and Marine Chemicals Division, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific and Industrial Research, G. B. Marg, Bhavnagar 364002, India
Suresh Kumar Kailasa Ionic Liquids Research Laboratory, Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat 395007, Gujarat, India
Naved I Malek Ionic Liquids Research Laboratory, Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat 395007, Gujarat, India.

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On the influence of metal nanoparticle and π-system sizes in the stability of noncovalent adducts: a theoretical study

Herein we have computationally evaluated the relationship between Ag and Au nanoparticle (Ag/AuNP) size and π-surface extension in the formation of noncovalent complexes at the PBE0-D3/def2-TZVP level of theory. The NP-π interaction is known in supramolecular chemistry as a Regium-π bond (Rg-π), and differentiates from classical coordination bonds in strength and type of metal orbitals involved. In this study, the Rg-π complexes involved small Ag/AuNPs composed by 1 to 5 atoms and benzene, naphthalene and anthracene as π-systems, being characterized using several molecular modeling tools, including molecular electrostatic potential (MEP) calculations, energy decomposition analysis (EDA), quantum theory of atoms in molecules (QTAIM), non covalent interaction plot (NCIplot) and natural bonding orbital (NBO) methodologies. We believe the results reported herein will be useful for those scientists working in catalysis, molecular recognition and materials science fields, where structural-energetic relationships of weak interactions are crucial to achieve product selectivity, a particular molecular recognition mode or a specific molecular assembly.

Tactfully regulating the ESIPT and TICT mechanism in the AIE-active multifunctional triphenylamine Schiff-base compound (TPASB) by methyl substitution

The triphenylamine Schiff-base (TPASB) with dual proton transfer sites (N1…H1-O1 [R1] and N2…H2-O2 [R2]), which is crucial in the field of optoelectronic materials. Herein, a novel molecular design strategy for preparing of TPASB-1 and TPASB-2 via the selective methylation of the hydroxyl group at the R2 or R1 position was proposed. The analysis of electronic structures and potential energy surfaces revealed that a single excited state intramolecular proton transfer (ESIPT) process of TPASB occurs only at R1. Nevertheless, the ESIPT process of TPASB-2 was successfully turned on at R2. More noteworthy is that compared to TPASB, the methylation of hydroxyl group at the R2 position triggers the TICT process of TPASB-1, effectively reducing the potential barrier of ESIPT at the R1 position. This theoretical study explains the role of the substituent effect in regulating ESIPT behaviour, and provides valuable guidance for synthesising efficacious ESIPT-active compounds.

Synthesis of a stable crystalline nitrene

Nitrenes are a highly reactive, yet fundamental, compound class. They possess a monovalent nitrogen atom and usually a short life span, typically in the nanosecond range. Here, we report on the synthesis of a stable nitrene by photolysis of the arylazide MSFluindN3 (1), which gave rise to the quantitative formation of the arylnitrene MSFluindN (2) (MSFluind is dispiro[fluorene-9,3'-(1',1',7',7'-tetramethyl-s-hydrindacen-4'-yl)-5',9''-fluorene]) that remains unchanged for at least 3 days when stored under argon atmosphere at room temperature. The extraordinary life span permitted the full characterization of 2 by single-crystal x-ray crystallography, electron paramagnetic resonance spectroscopy, and superconducting quantum interference device magnetometry, which supported a triplet ground state. Theoretical simulations suggest that in addition to the kinetic stabilization conferred by the bulky MSFluind aryl substituent, electron delocalization across the central aromatic ring contributes to the electron stabilization of 2.

DFT/MM Simulations for Cycloreversion Reaction of Cyclobutane Pyrimidine Dimer with Deprotonated and Protonated E283

DNA photolyase targets the primary ultraviolet (UV)-induced DNA lesion─cyclobutane pyrimidine dimer (CPD), attaches to it, and catalyzes its dissociation. The catalytic mechanism of DNA photolyase and the role of the conserved residue E283 remain subjects of debate. This study employs two-dimensional potential energy surface maps and minimum free energy paths calculated at the ωB97XD/6-31G/MM level to elucidate these mechanisms. Results suggest that the catalytic process follows a sequential, stepwise reaction in which the C5-C5 and C6-C6 bonds are cleaved in order, facilitated by a protonated E283. Activation free energies for these cleavages are calculated at 4.4 and 4.2 kcal·mol-1, respectively. Protonation of E283 reduces electrostatic repulsion with CPD and forms dual hydrogen bonds with it and provides better solvation, stabilizing the CPD radical anion, particularly during intermediate state. This stabilization renders the initial splitting step exergonic, slows reverse reactions of the C5-C5 bond cleavage and electron transfer, and ensures a high quantum yield. Furthermore, the protonation state of E283 significantly affects the type of bond cleavage. Other residues in the active site were also investigated for their roles in the mechanism.

Insight into the Metal-Involving Chalcogen Bond in the PdII/PtII-Based Complexes: Comparison with the Conventional Chalcogen Bond

The metal-involving Ch···M chalcogen bond and the conventional Ch···O chalcogen bond between ChX2 (Ch = Se, Te; X = CCH, CN) acting as a Lewis acid and M(acac)2 (M = Pd, Pt; Hacac = acetylacetone) acting as a Lewis base were studied by density functional theory calculations. It has been observed that the nucleophilicity of the PtII complexes is higher than that of the corresponding PdII complexes. As a result, the PtII complexes tend to exhibit a more negative interaction energy and larger orbital interaction. The strength of the chalcogen bond increases with the increase of the chalcogen atom and the electronegativity of the substituent on the Lewis acid and vice versa. The metal-involving chalcogen bond shows a typical weak closed-shell noncovalent interaction in the (HCC)2Ch···M(acac)2 complexes, while it exhibits a partially covalent nature in the (NC)2Ch···M(acac)2 complexes. The conventional Ch···O chalcogen bond displays the character of a weak noncovalent interaction, and its strength is generally weaker than that of metal-involving Ch···M interactions. It could be argued that the metal-involving chalcogen bond is primarily determined by the correlation term, whereas the conventional chalcogen bond is mainly governed by the electrostatic interaction.

Theoretical insights into enantioselective [2 + 1] cyclopropanation reactions of diazo compounds with electron-deficient olefins

CONTEXT

The cyclopropane skeleton plays a significant role in bioactive  molecules due to its distinctive structural properties. This has sparked keen interest and in-depth exploration in the field of stereoselective synthesis of cyclopropane derivatives. In the present study, the mechanism and the origin of stereoselectivity of diastereodivergent synthesis of cyclopropane derivatives via the catalyst-free [2 + 1]-cyclopropanation reactions of 3-diazo-N-methylindole (R1) with two types of electron-deficient olefins (R2 and R3) in both aqueous and toluene media have been studied using the DFT calculations. The findings indicate that these [2 + 1] cycloaddition reactions proceed in two stages, where the first step is not only the rate-determining step but also critically dictates the stereoselectivity of the product. The calculated diastereomeric ratios are in agreement with the experimental results. Furthermore, by utilizing non-covalent interaction (NCI) analysis and energy decomposition analysis based on molecular force fields (EDA-FF), we elucidated that the electrostatic interactions between reactant fragments in the transition state TS1s for the first step are the predominant factors determining the stereoselectivity, as opposed to the experimentally hypothesized steric hindrance and π-π stacking interactions.

METHODS

The geometrical structures of all minima and transition states on the potential energy surface (PES) in solvents water and toluene were fully optimized using the DFT method at the M06-2X(D3)/SMD/6-31 + G(d,p) level of theory. Single-point energy calculations were carried out based on the optimized geometries in the solution at the M06-2X(D3)/6-311 + G(d,p) level. All the DFT calculations were performed using the Gaussian 09 software. The optimized molecular structures were visualized using CYLview software. NCI analysis was performed using the Multiwfn and VMD softwares. The Multiwfn program was also used for CDFT and EDA-FF analyses.

Molecular dynamics simulations in pre-polymerization mixtures for peptide recognition

CONTEXT

Molecularly imprinted polymers (MIPs) have promising applications as synthetic antibodies for protein and peptide recognition. A critical aspect of MIP design is the selection of functional monomers and their adequate proportions to achieve materials with high recognition capacity toward their targets. To contribute to this goal, we calibrated a molecular dynamics protocol to reproduce the experimental trends in peptide recognition of 13 pre-polymerization mixtures reported in the literature for the peptide toxin melittin.

METHODS

Three simulation conditions were tested for each mixture by changing the box size and the number of monomers and cross-linkers surrounding the template in a solvent-explicit environment. Fully atomistic MD simulations of 350 ns were conducted with the AMBER20 software, with ff19SB parameters for the peptide, gaff2 parameters for the monomers and cross-linkers, and the OPC water model. Template-monomer interaction energies under the LIE approach showed significant differences between high-affinity and low-affinity mixtures. Simulation systems containing 100 monomers plus cross-linkers in a cubic box of 90 Å3 successfully ranked the mixtures according to their experimental performance. Systems with higher monomer densities resulted in non-specific intermolecular contacts that could not account for the experimental trends in melittin recognition. The mixture with the best recognition capacity showed preferential binding to the 13-26-α-helix, suggesting a relevant role for this segment in melittin imprinting and recognition. Our findings provide insightful information to assist the computational design of molecularly imprinted materials with a validated protocol that can be easily extended to other templates.

σ-Hole, lone-pair-hole, and π-hole site-based interactions in aerogen-comprising complexes: a comparative study

Herein, the potential of ZO3 and ZF2 aerogen-comprising molecules (where Z = Ar, Kr, and Xe) to engage in σ-, lp-, and π-hole site-based interactions was comparatively studied using various ab initio computations. For the first time, a premier in-depth elucidation of the external electric field (EEF) influence on the strength of the σ-, lp-, and π-hole site-based interactions within the ZO3/ZF2⋯NH3 and ⋯NCH complexes was addressed using oriented EEF with disparate magnitude. Upon the energetic features, σ-hole site-based interactions were noticed with the most prominent preferability in comparison to lp- and π-hole analogs. This finding was ensured by the negative interaction energy values of -11.65, -3.50, and -2.74 kcal mol-1 in the case of σ-, lp-, and π-hole site-based interactions within the XeO3⋯ and XeF2⋯NH3 complexes, respectively. Detailedly, the strength of the σ- and lp-hole site-based interactions directly correlated with the atomic size of the aerogen atoms and the magnitude of the positively oriented EEF. Unexpectedly, an irregular correlation was noticed for the interaction energies of the π-hole site-based interactions with the size of the π-hole. Interestingly, the π-hole site-based interactions within Kr-comprising complexes exhibited higher negative interaction energies than the Ar- and Xe-comprising counterparts. Notwithstanding, a direct proportion between the interaction energies of the π-hole site-based interactions and π-hole size was obtained by employing EEF along the positive orientation with high strength. The present outcomes would be a fundamental basis for forthcoming progress in studying the σ-, lp-, and π-hole site-based interactions within aerogen-comprising complexes and their pertinent applications in materials science and crystal engineering.

Manganese matere bonds in biological systems: PDB inspection and DFT calculations

A Protein Data Bank (PDB) survey has revealed noncovalent contacts involving Mn centres and protein residues. Their geometrical features are in line with the interaction between low electron density sites located along the Mn-O/N coordination bonds (σ-holes) and the lone pairs belonging to TYR, SER or HIS residues, known as a matere bond (MaB). Calculations at the PBE0-D3/def2-TZVP level of theory were used to investigate the strength and shed light on the physical nature of the interaction. We expect the results presented herein will be useful for those scientists working in the fields of bioinorganic chemistry, particulary in protein-metal docking, by providing new insights into transition metal⋯Lewis base interactions as well as a retrospective point of view to further understand the structural and functional implications of this key transition metal ion.

Carbene-Catalyzed and Pnictogen Bond-Assisted Access to PIII-Stereogenic Compounds

Intermolecular pnictogen bonding (PnB) catalysis has received increased interest in non-covalent organocatalysis. It has been demonstrated that organic electron-deficient pnictogen atoms can act as prospective Lewis acids. Here, we present a catalytic approach for the asymmetric synthesis of chiral PIII compounds by combining intramolecular PnB interactions and carbene catalysis. Our design features a pre-chiral phosphorus molecule bearing two electron-withdrawing benzoyl groups, resulting in the formation of a σ-hole at the P atom. X-ray and non-covalent interaction (NCI) analysis indicate that the model substrates exhibit intrinsic PnB interaction between the oxygen atom of the formyl group and the phosphorus atom. This induces a conformational locking effect, leading to the crystallization of the phosphorus substrate in a preferred conformation (P212121 chiral group). Under the catalysis of N-heterocyclic carbene, the aldehyde moiety activated by the pnictogen bond selectively reacts with an alcohol to yield the corresponding chiral monoester/phosphorus product with excellent enantioselectivity. This Lewis acidic phosphorus center, aroused by the non-polarized intramolecular pnictogen bond interaction, assists in conformational and selective regulations, providing unique opportunities for catalysis and beyond.

Chalcogen Noncovalent Interactions between Diazines and Sulfur Oxides in Supramolecular Circular Chains

The noncovalent chalcogen interaction between SO2/SO3 and diazines was studied through a dispersion-corrected DFT Kohn-Sham molecular orbital together with quantitative energy decomposition analyses. For this, supramolecular circular chains of up to 12 molecules were built with the aim of checking the capability of diazine molecules to detect SO2/SO3 compounds within the atmosphere. Trends in the interaction energies with the increasing number of molecules are mainly determined by the Pauli steric repulsion involved in these σ-hole/π-hole interactions. But more importantly, despite the assumed electrostatic nature of the involved interactions, the covalent component also plays a determinant role in its strength in the involved chalcogen bonds. Noticeably, π-hole interactions are supported by the charge transfer from diazines to SO2/SO3 molecules. Interaction energies in these supramolecular complexes are not only determined by the S···N bond lengths but attractive electrostatic and orbital interactions also determine the trends. These results should allow us to establish the fundamental characteristics of chalcogen bonding based on its strength and nature, which is of relevance for the capture of sulfur oxides.

In Silico Design and Characterization of a New Molecular Electride: Li@Calix[3]Pyrrole

Electrides, in which anionic electrons are localized independently of the atoms in the compound, have shown promise, especially as catalysts and optoelectronic materials. Here, we present a new computationally designed molecular electride, Li@calix[3]pyrrole (Li@C3P). Electron density and electron localization function analyses unequivocally confirm the existence of localized electride electron density, outside the system, independent of any specific atoms. Non-covalent interaction plots further validate the character of the isolated localized electron, suggesting that the system can be accurately represented by Li+@calix[3]pyrrole ⋅ e-, denoting its distinct charge separation. The remarkable non-linear optical properties of Li@C3P, including average polarizability,α ‾ ${\bar{\alpha }}$ =412.4 au, first hyperpolarizability, β=4.46×104 au, and second hyperpolarizability,γ ∥ ${{\gamma }_{\parallel }}$ =18.40×106 au, are unparalleled in the previously reported and similar Li@C4P molecular electride. Furthermore, energy decomposition analysis in combination with natural orbital for chemical valence theory sheds light on the mechanism of electron density transfer from Li to the C3P cage, yielding the charge-separated Li@C3P complex. In addition to the electron transfer, a key factor to its electride nature is the electronic structure of the CnP cage, which has its lowest unoccupied molecular orbital located in the void adjacent to the N-H groups at the back of the bowl-shaped CnP cage.

Exploring the Reactivity of Rigid 1-Azadienes Derived from Methylene γ-Lactams. Applications to the Stereoselective Synthesis of Spiro-γ-Lactams

A study on the reactivity of rigid 1-azadienes derived from methylene γ-lactams is reported. Through the functionalization of 1-amino α,β-unsaturated γ-lactam derivatives, easily available from a multicomponent reaction of amines, aldehydes, and pyruvates, it is possible to in situ generate rigid 1-azadienes locked by a γ-lactam core. The 4π-electron system of those rigid 1-azadienes can behave as both diene and dienophile species through a spontaneous cyclodimerization reaction or exclusively as dienes or dienophiles if they are trapped with imines or cyclopentadiene, respectively. The use of chiral rigid 1-azadienes as dienophiles in the cycloaddition reaction with cyclopentadiene leads to the formation of spiro-γ-lactams bearing four stereogenic centers in a highly stereospecific manner, reporting the first example of the use of methylene-γ-lactams in the synthesis of spirocycles.

From Chalcogen Bonding to S-π Interactions in Hybrid Perovskite Photovoltaics

The stability of hybrid organic-inorganic halide perovskite semiconductors remains a significant obstacle to their application in photovoltaics. To this end, the use of low-dimensional (LD) perovskites, which incorporate hydrophobic organic moieties, provides an effective strategy to improve their stability, yet often at the expense of their performance. To address this limitation, supramolecular engineering of noncovalent interactions between organic and inorganic components has shown potential by relying on hydrogen bonding and conventional van der Waals interactions. Here, the capacity to access novel LD perovskite structures that uniquely assemble through unorthodox S-mediated interactions is explored by incorporating benzothiadiazole-based moieties. The formation of S-mediated LD structures is demonstrated, including one-dimensional (1D) and layered two-dimensional (2D) perovskite phases assembled via chalcogen bonding and S-π interactions, through a combination of techniques, such as single crystal and thin film X-ray diffraction, as well as solid-state NMR spectroscopy, complemented by molecular dynamics simulations, density functional theory calculations, and optoelectronic characterization, revealing superior conductivities of S-mediated LD perovskites. The resulting materials are applied in n-i-p and p-i-n perovskite solar cells, demonstrating enhancements in performance and operational stability that reveal a versatile supramolecular strategy in photovoltaics.

Formation of chalcogen-bonding interactions and their role in the trans-trans conformation of thiourea

The chalcogen-bonding interactions formed at both sides of the thiocarbonyl group in thiourea were investigated. In particular, the role of these chalcogen-bonding interactions in the trans-trans conformation of thiourea was evaluated via single-crystal X-ray diffraction analysis and DFT calculations. The obtained results indicate that the Se⋯S⋯Se dual chalcogen-bonding interactions play a stronger role in controlling the planar structure than the S⋯S⋯S interactions.

Synthesis of Aza[n]helicenes up to n = 19: Hydrogen-Bond-Assisted Solubility and Benzannulation Strategy

Synthetic challenges toward anomalous structures and electronic states often involve handling problems such as insolubility in common organic solvents and oxidative degradation under aerobic conditions. We designed benzo-annulated aza[n]helicenes, which benefit from both the suppressed elevation of highest occupied molecular orbital (HOMO) energies and high solubility due to hydrogen bonding with solvent molecules to overcome these challenges. This strategy enabled the synthesis of six new aza[n]helicenes ([n]AHs) of different lengths (n = 9-19) from acyclic precursors via one-pot intramolecular oxidative fusion reactions. The structures of all of the synthesized aza[n]helicenes were determined by X-ray diffraction (XRD) analysis, and their electrochemical potentials were measured by cyclic voltammetry. Among the synthesized aza[n]helicenes, [17]AH and [19]AH are the first heterohelicenes with a triple-layered helix. The noncovalent interaction (NCI) plots confirm the existence of an effective π-π interaction between the layers. The absorption and fluorescence spectra red-shifted as the helical lengths increased, without any distinct saturation points. The optical resolutions of N-butylated [9]AH, [11]AH, [13]AH, and [15]AH were accomplished, and their circular dichroism (CD) and circularly polarized luminescence (CPL) were measured. Thus, the structural, (chir)optical, and electrochemical properties of the aza[n]helicenes were comprehensively analyzed.

Study on Pyridine-Boryl Radical-Promoted, Ketyl Radical-Mediated Carbon-Carbon Bond-Forming Reactions

Ketyl radicals are synthetically versatile reactive species, but their applications have been hampered by harsh generation conditions employing highly reducing metals. Recently, the pyridine-boryl radical received wide attention as a promising organic reductant because of its mildness as well as convenience in handling. While probing the utility of the pyridine-boryl radical, our group observed facile pinacol coupling reactivity that had not been known at that time. This serendipitous finding was successfully rendered into a practical synthesis of tetraaryl-1,2-diols in up to 99% yield within 1 h. Subsequently, upon examinations of various reaction manifolds, a diastereoselective ketyl-olefin cyclization was accomplished to produce cycloalkanols such as trans-2-alkyl-1-indanols. Compared to the previous methods, the stereocontrolling ability was considerably enhanced by taking advantage of the structurally modifiable boryl group that would be present near the bond-forming site. In this full account, our synthetic efforts with the O-boryl ketyl radicals are disclosed in detail, covering the discovery, optimization, scope expansion, and mechanistic analysis, including density functional theory (DFT) calculations.

Disentangling the Conformational Space and Structural Preferences of Tetrahydrofurfuryl Alcohol Using Rotational Spectroscopy and Computational Chemistry

The influence of the hydroxymethyl (CH2OH) group on the tetrahydrofuran (THF) ring structure was investigated by disentangling the gas phase conformational landscape of the sugar analogue tetrahydrofurfuryl alcohol (THFA). By combining rotational spectroscopy (6-20 GHz) and quantum chemical calculations, transitions corresponding to two stable conformers of THFA and their 13C isotopologues were observed and assigned in the rotational spectrum. The positions of the C atoms were precisely determined to unambiguously distinguish between nearly isoenergetic pairs of conformers that differ in their ring configurations: envelope (E) versus twist (T). The rotational spectrum confirms that the E ring geometry is favoured when the CH2OH fragment lies gauche (-) to the THF backbone (OCCO ~-60°) whereas the T form is more stable for the gauche (+) alignment of the substituent (OCCO ~+60°). The observed spectral intensities suggest that conformational relaxation of the THF geometry (E↔T) to the more stable form readily occurs within the pairs of g- and g+ conformers which is consistent with the low barriers (1.5-1.7 kJ mol-1) for conversion determined via transition state calculations. Insights into the intramolecular hydrogen bonding and other weak interactions stabilizing the lowest energy structures of THFA were derived and rationalized using non-covalent interaction analyses.

How the addition of atomic hydrogen to a multiple bond can be catalyzed by water molecules

Observational data show complex organic molecules in the interstellar medium (ISM). Hydrogenation of small unsaturated carbon double bond could be one way for molecular complexification. It is important to understand how such reactivity occurs in the very cold and low-pressure ISM. Yet, there is water ice in the ISM, either as grain or as mantle around grains. Therefore, the addition of atomic hydrogen on double-bonded carbon in a series of seven molecules have been studied and it was found that water catalyzes this reaction. The origin of the catalysis is a weak charge transfer between the π MO of the unsaturated molecule and H atom, allowing a stabilizing interaction with H2O. This mechanism is rationalized using the non-covalent interaction and the quantum theory of atoms in molecules approaches.

N···C═O n → π* Interaction: Gas-Phase Electronic and Vibrational Spectroscopy Combined with Quantum Chemistry Calculations

Herein, we have used gas-phase electronic and vibrational spectroscopic techniques for the first time to study the N···C═O n → π* interaction in ethyl 2-(2-(dimethylamino) phenyl) acetate (NMe2-Ph-EA). We have measured the electronic spectra of NMe2-Ph-EA in the mass channels of its two distinct fragments of m/z = 15 and 192 using a resonant two-photon ionization technique as there was extensive photofragmentation of NMe2-Ph-EA. Identical electronic spectra obtained in the mass channels of both fragments confirm the dissociation of NMe2-Ph-EA in the ionic state, and hence, the electronic spectrum of the fragment represents that of NMe2-Ph-EA only. UV-UV hole-burning spectroscopy proved the presence of a single conformer of NMe2-Ph-EA in the experiment. Detailed quantum chemistry calculations reveal the existence of a N···C═O n → π* interaction in all six low-energy conformers of NMe2-Ph-EA. A comparison of the IR spectrum of NMe2-Ph-EA acquired from the gas-phase experiment with those obtained from theoretical calculations indicates that the experimentally observed conformer has a N···C═O n → π* interaction. The present finding might be further valuable in drug design and their recognition based on the N···C═O n → π* interaction.

Using Hybrid PDI-Fe3O4 Nanoparticles for Capturing Aliphatic Alcohols: Halogen Bonding vs. Lone Pair-π Interactions

In this study, Fe3O4 nanoparticles (FeNPs) decorated with halogenated perylene diimides (PDIs) have been used for capturing VOCs (volatile organic compounds) through noncovalent binding. Concretely, we have used tetrachlorinated/brominated PDIs as well as a nonhalogenated PDI as a reference system. On the other hand, methanol, ethanol, propanol, and butanol were used as VOCs. Experimental studies along with theoretical calculations (the BP86-D3/def2-TZVPP level of theory) pointed to two possible and likely competitive binding modes (lone pair-π through the π-acidic surface of the PDI and a halogen bond via the σ-holes at the Cl/Br atoms). More in detail, thermal desorption (TD) experiments showed an increase in the VOC retention capacity upon increasing the length of the alkyl chain, suggesting a preference for the interaction with the PDI aromatic surface. In addition, the tetrachlorinated derivative showed larger VOC retention times compared to the tetrabrominated analog. These results were complemented by several state-of-the-art computational tools, such as the electrostatic surface potential analysis, the Quantum Theory of Atoms in Molecules (QTAIM), as well as the noncovalent interaction plot (NCIplot) visual index, which were helpful to rationalize the role of each interaction in the VOC···PDI recognition phenomena.

Mixing water, sugar, and lipid: Conformations of isolated and micro-hydrated glycolipids in the gas phase

Both sugars and lipids are important biomolecular building blocks with exceptional conformational flexibility and adaptability to their environment. Glycolipids bring together these two molecular components in the same assembly and combine the complexity of their conformational landscapes. In the present study, we have used selective double resonance vibrational spectroscopy, in combination with a computational approach, to explore the conformational preferences of two glycolipid models (3-0-acyl catechol and guaiacol α-D-glucopyranosides), either fully isolated in the gas phase or controlled interaction with a single water molecule. We could identify the preferred conformation and structures of the isolated and micro-hydrated species and evidence of the presence of a strong water pocket, which may influence the conformational flexibility of such systems, even in less controlled environments.

Frustrated Lewis pair-mediated hydro-dehalogenation: crucial role of non-covalent interactions

CONTEXT

Organic halides stand as invaluable reagents with diverse applications in synthetic chemistry and various industrial processes. Despite their utility, concerns arise due to their inherent toxicity. Addressing these apprehensions, hydro-dehalogenation has emerged as a promising strategy involving the replacement of halogen atoms with hydrogen atoms to transform toxic organic halides into hydrocarbons. This study delves into the computational exploration of hydro-dehalogenation reactions of benzyl halide, mediated by frustrated Lewis pairs (FLPs), using density functional theory (DFT). The reactions entail the formation of FLP1 or FLP2 in the presence of TMP or lutidine with B(C6F5)3, respectively. This is followed by heterolytic cleavage of dihydrogen and subsequent reaction with benzyl halides. Non-covalent interaction analysis underscores the significance of π-π stacking and CH-π interactions in stabilizing transition states. Additionally, the activation strain model (ASM) dissects activation energies, revealing the substantial impact of strain energy on reaction barriers. Energy decomposition analysis (EDA) offers insights into the contributions of electrostatic, orbital, and dispersion energies to the overall attractive interaction energy. The investigation extends to hydro-dehalogenation reactions of ethyl halides, uncovering distinct mechanisms and activation barriers. This comprehensive analysis illuminates the intricacies of hydro-dehalogenation reactions, providing valuable insights into their mechanisms and paving the way for future studies in this field.

METHODS

Geometry optimizations were carried out at the M06-2X/def2-SVP level of theory, which was performed using the Gaussian 16 program. Solvent-corrected single-point energies were also calculated using the polarizable continuum model (PCM) at the PCM(chloroform)-M06-2X/def2-TZVP//M06-2X/def2-SVP level of theory. The Gibbs free energy correction was determined from computations performed at the M06-2X/def2-SVP level of theory. Principal interacting orbital (PIO) analysis was conducted using the NBO 6.0 software. The nature of bonding in the respective transition state (TS) structures was analyzed using atoms-in-molecules (AIM) analyses. Additionally, the presence of non-covalent interactions (NCI) was exemplified using Multiwfn software.

Screening the Optimal Probe by Expounding the ESIPT Mechanism and Photophysical Properties in Bis-HBX with Multimodal Substitutions

DFT and TD-DFT were used in this article to investigate the effects of different substitutions at multiple sites on the photophysical mechanism of bis-HBX in the gas phase. Four different substitution modes were selected, denoted as A1 (X=Me, Y=S), A2 (X=OMe, Y=S), B1 (X=Me, Y=NH), and C1 (X=Me, Y=O). The geometric parameters proved that the IHBs enhanced after photoexcitation, which was conducive to promote the ESIPT process. Combining the analysis of the PECs, it was revealed that the bis-HBX molecule underwent the ESIPT process, and the ease of the ESIPT process was in the order of A1 > A2> B1 > C1. In particular, the TICT process in A1 and B1 promoted the occurrence of the ESIPT process. In addition, the IC process was identified, particularly in C1. Meanwhile, the calculation of fluorescence lifetime and fluorescence rate further confirmed that A1 was the most effective fluorescent probe molecule. This theoretical research provides an innovative theoretical reference for regulating ESIPT reactions and optimizing fluorescent probe molecules.

Supramolecular assembly of amphiphilic platinum(ii) Schiff base complexes: diverse spectroscopic changes and nanostructures through rational molecular design and solvent control

A new class of amphiphilic tetradentate platinum(ii) Schiff base complexes has been designed and synthesized. The self-assembly properties by exploiting the potential Pt⋯Pt interactions of amphiphilic platinum(ii) Schiff base complexes in the solution state have been systematically investigated. The presence of Pt⋯Pt interactions has further been supported by computational studies and non-covalent interaction (NCI) analysis of the dimer of the complex. The extent of the non-covalent Pt⋯Pt and π-π interactions could be regulated by a variation of the solvent compositions and the hydrophobicity of the complexes, which is accompanied by attractive spectroscopic and luminescence changes and leads to diverse morphological transformations. The present work represents a rare example of demonstration of directed cooperative assembly of amphiphilic platinum(ii) Schiff base complexes by intermolecular Pt⋯Pt interactions in solution with an in-depth mechanistic investigation, providing guiding principles for the construction of supramolecular structures with desirable properties using platinum(ii) Schiff base building blocks.

Bicarbonate-binding catalysis for the enantioselective desymmetrization of keto sulfonium salts

Herein, an enantioselective desymmetrization of cyclic keto sulfonium salts through enantioselective deprotonation/ring opening process by anion-binding catalysis is presented. We report a squaramide/HCO3- complex as catalytic active species which is able to stereo-differentiate two enantiomeric protons, triggering the ring opening event taking advantage of the great tendency of sulfonium salts to act as leaving groups. Thus, this desymmetrization methodology give rise to β-methylsulfenylated sulfa-Michael addition type products with excellent yields and very good enantioselectivities. The bifunctional organocatalyst has been demonstrated to be capable of activating simultaneously the base and the keto sulfonium salt by DFT calculations and experimental proofs.

Guest-Responsive Near-Infrared-Luminescent Metal-Organic Cage Organized by Porphyrin Dyes and Yb(III) Complexes

Metal-organic cages (MOCs) with luminophores have significant advantages for the facile detection of specific molecules based on turn-on or turn-off luminescence changes induced by host-guest complexation. One important challenge is the development of turn-on-type near-infrared (NIR)-luminescent MOCs. In this study, we synthesized a novel MOC consisting of two porphyrin dyes linked by four Yb(III) complexes, which exhibit bimodal red and NIR fluorescence signals upon photoexcitation of the porphyrin π system. Single-crystal X-ray structural analysis and computational molecular modeling revealed that planar aromatic perfluorocarbons were intercalated into the MOC. The tight packing between the MOC and guests enhanced the NIR fluorescence of Yb(III) by suppressing energy transfer from the photoexcited porphyrin to oxygen molecules. Guest-responsive turn-on NIR fluorescence changes in an MOC were successfully demonstrated.

Structural, computational and in silico studies of 4-bromo-3-flurobenzonitrile as anti-Alzheimer and anti-Parkinson agents

A novel dimer of the 4-bromo-3-fluorobenzonitrile was crystallized and studied using a spectroscopic method such as the scanning electron microscope method. The computational simulations substantiated the structural analysis findings. The Hirshfeld surface analysis has been performed for visualizing, exploring and quantifying the intra and inter-molecular interactions that stabilize the crystal packing of the compound. The NBO and QTAIM analyses were applied to study the nature and origin of the attractive forces involved in the crystal structure. Further, the pharmacokinetic properties of the compound were evaluated, indicating good brain-blood barrier and central nervous system penetration capability. Hence, in silico studies was carried out to explore the binding pattern of the titled compound against acetylcholinesterase and butyrylcholinesterase, and tumor necrosis factor-alpha converting enzyme proteins using molecular docking and molecular dynamics simulations approach. Further, the titled compound is compared with standard drugs through molecular docking studies. The in silico studies finally predicts that the compound under investigation may act as a good inhibitor for treating Alzheimer's disease and further in vitro and in vivo studies may provide its therapeutic potential.Communicated by Ramaswamy H. Sarma.

Selective recognition between aromatics and aliphatics by cage-shaped borates supported by a machine learning approach

Selective recognition between hydrocarbon moieties is a longstanding issue. Although we developed a π-pocket Lewis acid catalyst with high selectivity for aromatic aldehydes over aliphatic ones, a general strategy for catalyst design remains elusive. As an approach that transfers the molecular recognition based on multiple cooperative non-covalent interactions within the π-pocket to a rational catalyst design, herein, we demonstrate Lewis acid catalysts showing improved selectivity through the support of an ensemble algorithm with random forest, Ada Boost, and XG Boost as a machine learning (ML) approach. Using 7963 explanatory variables extracted from model hetero-Diels-Alder reactions, the ensemble algorithm predicted the chemoselectivity of unlearned catalysts. Experiments confirmed the prediction. The proposed catalyst shows the highest selective recognition, reminiscing enzymatic catalytic activity. Additionally, a SHapley Additive exPlanations (SHAP) method suggested that the selectivity originates from the polarizability and three-dimensional size of the catalyst. This insight leads to rational design guidelines for Lewis acid catalysts with dispersion forces.

Encapsulation of charged halogens by the 512 water cage

This study focuses on the encapsulation of the entire series of halides by the 512 cage of twenty water molecules and on the characterization of water to water and water to anion interactions. State-of-the-art computations are used to determine equilibrium geometries, energy related quantities, and thermal stability towards dissociation and to dissect the nature and strength of intermolecular interactions holding the clusters as stable units. Two types of structures are revealed: heavily deformed cages for F- indicating a preference for microsolvation, and slightly deformed cages for the remaining anions indicating a preference for encapsulation. The primary variable dictating the properties of the clusters is the charge density of the central halide, with the most severe effects observed for the F- case. For the remaining halides, the anion may be safely viewed as a sort of "big electron" with little local disruptive power, enough to affect the network of non-covalent hydrogen bonds in the cage, but not enough to break it. Gibbs energies for dissociation either into cavity and halide or into water molecules and halide suggest that, in a similar way as to methane clathrate, a more weakly bonded complex that has been detected in the gas phase, all halide containing clathrate-like structures should be amenable to experimental detection in the gas phase at moderate temperature and pressure conditions.

Scaffold-Oriented Asymmetric Catalysis: Conformational Modulation of Transition State Multivalency during a Catalyst-Controlled Assembly of a Pharmaceutically Relevant Atropisomer

A new class of superbasic, bifunctional peptidyl guanidine catalysts is presented, which enables the organocatalytic, atroposelective synthesis of axially chiral quinazolinediones. Computational modeling unveiled the conformational modulation of the catalyst by a novel phenyl urea N-cap, that preorganizes the structure into the active, folded state. A previously unanticipated noncovalent interaction involving a difluoroacetamide acting as a hybrid mono- or bidentate hydrogen bond donor emerged as a decisive control element inducing atroposelectivity. These discoveries spurred from a scaffold-oriented project inspired from a fascinating investigational BTK inhibitor featuring two stable chiral axes and relies on a mechanistic framework that was foreign to the extant lexicon of asymmetric catalysis.

Increased Absorption of Thyroxine in a Murine Model of Hypothyroidism Using Water/CO2 Nanobubbles

Thyroxine (T4) is a drug extensively utilized for the treatment of hypothyroidism. However, the oral absorption of T4 presents certain limitations. This research investigates the efficacy of CO2 nanobubbles in water as a potential oral carrier for T4 administration to C57BL/6 hypothyroid mice. Following 18 h of fasting, the formulation was administered to the mice, demonstrating that the combination of CO2 nanobubbles and T4 enhanced the drug's absorption in blood serum by approximately 40%. To comprehend this observation at a molecular level, we explored the interaction mechanism through which T4 engages with the CO2 nanobubbles, employing molecular simulations, semi-empirical quantum mechanics, and PMF calculations. Our simulations revealed a high affinity of T4 for the water-gas interface, driven by additive interactions between the hydrophobic region of T4 and the gas phase and electrostatic interactions of the polar groups of T4 with water at the water-gas interface. Concurrently, we observed that at the water-gas interface, the cluster of T4 formed in the water region disassembles, contributing to the drug's bioavailability. Furthermore, we examined how the gas within the nanobubbles aids in facilitating the drug's translocation through cell membranes. This research contributes to a deeper understanding of the role of CO2 nanobubbles in drug absorption and subsequent release into the bloodstream. The findings suggest that utilizing CO2 nanobubbles could enhance T4 bioavailability and cell permeability, leading to more efficient transport into cells. Additional research opens the possibility of employing lower concentrations of this class of drugs, thereby potentially reducing the associated side effects due to poor absorption.

Metal-Induced Enhancement of Tetrel Bonding. The Case of C⋅⋅⋅X-IrIII (X=Cl, Br) Tetrel Bond Involving a Methyl Group

In X-ray structures of the isomorphic mer-[IrX3(THT)(CNXyl)2] (X=Cl 1, Br 2; THT=tetrahydrothiophene; Xyl=2,6-Me2C6H3-) complexes, we revealed short intermolecular contacts between the C-atom of an isocyanide methyl group and halide ligands of another molecule. Geometrical consideration of the X-ray data and analysis of appropriate DFT studies allowed the attribution of these contacts to CMe⋅⋅⋅X-IrIII (X=Cl, Br) tetrel bond. Specifically, through the application of DFT calculations and various theoretical models, the presence of tetrel bonding interactions was validated, and the contribution of the CMe⋅⋅⋅X-IrIII interaction was assessed. The reinforcement of the tetrel bond upon the isocyanide coordination to iridium(III) is substantiated by molecular electrostatic potential (MEP) surface calculations. To distinguish the tetrel bonding characteristics of CMe⋅⋅⋅X-IrIII (X=Cl, Br) interactions from conventional hydrogen bonding, we employed multiple computational methodologies, including Natural Bond Orbital (NBO) analysis and Electron Localization Function (ELF) analysis. Additionally, Energy Decomposition Analysis (EDA) was applied to selected model systems to explore the underlying physical nature of these interactions.

Stability trends in carbocation intermediates stemming from germacrene A and hedycaryol

In the current work, we analyzed the origin of difference in stabilities among the germacrene A and hedycaryol-derived carbocations. This study focused on twelve hydrocarbons derived from germacrene A and twelve from hedycaryol, which can be divided into three groups: four molecules containing 6-6 bicyclic rings, four 5-7 bicyclic compounds with the carbocation being on the seven-membered ring and the remaining four 5-7 bicyclic compounds with the carbocation on the five-membered ring. The variations in energy within the groups of carbocations (i.e., 6-6 and two kinds of 5-7 bicyclic carbocations) can be ascribed to intramolecular repulsion interactions, as seen from non-covalent interactions plots. Despite the structural similarities between germacrene A and hedycaryol cations, they possess a somewhat different stability trend. These differences are attributed to C+···OH intramolecular interactions present in some hedycaryol cations, which are absent in the carbocations derived from germecrene A.

Molecular Hydrogen Acts as a Hydrogen Bond Proton Acceptor: From Protonated Betaine Tagging to the Weakest Hydrogen Bond

In an attempt to gain further insights into the intermolecular interactions implied by Rizzo's group's cautionary tale related to molecular tagging in infrared multiple photon dissociation (IRMPD) spectroscopy with molecular messengers [Masson, A. . J. Chem. Phys. 2015, 143, 104313], in the present study, we provide an in-depth analysis of the noncovalent interaction between the molecular hydrogen and protonated betaine molecule in the gas phase. We aim to shed some new light on the fundamental issues concerning the wide diapason of hydrogen-bonding-type intermolecular interactions, with a wide variety of proton acceptors. We demonstrate that in the course of tagging the protonated betaine with molecular hydrogen from the OH group side, it is the σ bond of molecular hydrogen that plays the role of hydrogen-bonding proton acceptor. The tagging thus induces a small yet significant red shift of the protonated betaine O-H stretching mode. We investigate the performance of a wide range of density functional theory (DFT) functionals for the calculation of anharmonic vibrational frequency shifts of the studied system, which are essential for the correct interpretation of the experimental IRMPD data. For an accurate prediction of the OH stretching frequency shifts, specifically designed functionals such as Handy's group HCTH/407 should be applied. The empirical dispersion correction enhances the systematic overestimation of the anharmonic frequency shift, characteristic of the most widely used DFT functionals. Combining the full-wave function approach with the charge field perturbation and natural bond orbital (NBO) deletion analyses, we demonstrate that the frequency shift in the OH-tagged structure is governed by the σHH → σ*OH intermolecular charge transfer. This interaction stabilizes the OH-tagged dimer as well, in contrast to the dipole-quadrupole electrostatic interaction energy term. Topological analysis of the electron density reveals the presence of an intermolecular bond critical point with a positive value of the density Laplacian very close to the lower limit for hydrogen bonds. NCI analyses demonstrate that the OH···H2 interaction is weaker than the intramolecular CH···O one within the protonated betaine molecule, with the through of reduced density gradient appearing at less negative sign(λ2)·ρ values. Analyzing the O-H stretching vibrational potential with the second-generation absolutely localized molecular orbitals energy decomposition analysis (ALMO-EDA 2) revealed that in the case of betaineH(+) tagged from the OH group side, the permanent electrostatics (ΔEelec), polarization (ΔEpol), and charge-transfer (ΔEct) contributions to the total intermolecular interaction energy contribute favorably to the weak hydrogen bond formation and to the red shift of the fundamental O-H stretching frequency, the ΔEct contribution being the most significant in the last context. The Pauli repulsion term, on the other hand, favors an O-H stretching frequency blue shift as a consequence of the vibrational confinement effects.

Cation-Stacking Approach Enabling Interconversion between Bis(xanthylium) and its Reduced Species

Cyclophane-type dications with two units of xanthylium were designed, with the expectation that intramolecular interaction between cation units could induce changes in absorption and redox behavior. The desired dications were synthesized via the macrocyclic diketone as a key intermediate, which was efficiently obtained by a stepwise etherification. X-ray and UV/Vis measurements revealed that the cyclophane-type dications adopt a stacking structure in both the crystal and solution. Due to the intramolecular interaction caused by π-π stacking of the xanthylium units, a considerable blue shift compared to the corresponding monocations and a two-stage one-electron reduction process were observed in the dications. Furthermore, upon electrochemical reduction of dications, the formation of biradicals via radical cation species was demonstrated by UV/Vis spectroscopy with several isosbestic points at both stages. Therefore, the cation-stacking approach is a promising way to provide novel properties due to perturbation of their molecular orbitals and to stabilize the reduced species even though they have open-shell characters.

Room Temperature Phosphorescence in Crystalline Iodinated Eumelanin Monomer

We report the room temperature phosphorescence upon iodination on a crystalline eumelanin monomer with shielded hydroxyl moieties, ethyl 5,6-dimethoxyindole-2-carboxylate (DMICE). Ultrafast intersystem crossing (ISC) is observed in the iodinated (IDMICE) as well as brominated (BDMICE) analogues of the eumelanin monomer derivative in solution. The triplet quantum yields (φT) and intersystem crossing rates (kISC) of the halogenated eumelanin derivatives areφ T B D M I C E ${{\phi{} }_{T}^{BDMICE}}$ =25.4±1.1 %;k I S C B D M I C E ${{k}_{ISC}^{BDMICE}}$ =1.95×109 s-1 andφ T I D M I C E ${{\phi{} }_{T}^{IDMICE}}$ =59.1±1.6 %;k I S C I D M I C E = ${{k}_{ISC}^{IDMICE}=}$ 1.36×1010 s-1, as monitored using transient absorption spectroscopy. Theoretical calculations based on nuclear ensemble method reveal that computed kISC and spin-orbit coupling matrix elements for eumelanin derivatives are larger for IDMICE relative to BDMICE. The halogen and π-π interactions, with distinct excitonic coupling and higher ISC rate promote phosphorescence in IDMICE molecular crystals. Accessing triplet excited states and resultant photoluminescence through structural modification of eumelanin scaffolds paves way for exploring the versatility of eumelanin-inspired molecules as bio-functional materials.

Metal free synthesis of thermally stable blue fluorescent m-terphenyls by ring transformation of 2H-pyran-2-ones: chemical synthesis, spectroscopy and computational studies

A simple yet convenient nucleophile-induced synthetic route for the construction of thermally stable fluorescent active functionalized stilbenes has been delineated. The nucleophile-induced base encouraged synthetic protocol was performed under mild conditions without harming the environment and products were achieved in good yields. The synthesized stilbenes showed amazing emission properties and good thermal stability. Synthesized products displayed interesting positive solvatochromism in different solvents based on variation in polarity. Further, we present a comprehensive analysis of the eight molecules, leveraging a combination of Density Functional Tight Binding (DFTB), Density Functional Theory (DFT) calculations, and Molecular Dynamics (MD) simulations. This integrated approach allowed for an in-depth exploration of the electronic structures, reactivity profiles, and dynamic behaviors of these complex molecular systems. Our findings reveal significant insights into the physicochemical properties of the synthesized molecules, contributing to a deeper understanding of their potential applications in various fields.

Photodissociation of leucine-enkephalin protonated peptide: an experimental and theoretical perspective

Understanding the competing processes that govern far ultraviolet photodissociation (FUV-PD) of biopolymers such as proteins is a challenge. Here, we report a combined experimental and theoretical investigation of FUV-PD of protonated leucine-enkephalin pentapeptide ([YGGFL + H]+) in the gas-phase. Time-dependent density functional theory (TD-DFT) calculations in combination with experiments and previous results for amino acids and shorter peptides help in rationalizing the evolution of the excited states. The results confirm that fragmentation of [YGGFL + H]+ results mainly from vibrationally excited species in the ground electronic state, populated after internal conversion. We also propose fragmentation mechanisms for specific photo-fragments such as tyrosine side chain loss (with an extra hydrogen) or hydrogen loss. In general, we observe the same mechanisms as for smaller peptides or protonated Tyr and Phe, that are not quenched by the presence of other amino acids. Nevertheless, we also found some differences, as for H loss, in part due to the fact that the charge is solvated by the peptide chain and not only by the COOH terminal group.