Estimating the energy of intramolecular bifurcated (three-centered) hydrogen bond by X-ray, IR and 1 H NMR spectroscopy, and QTAIM calculations

Evidence for the O-H⋅⋅⋅O=C Resonance-Assisted Hydrogen Bond in Tropolones and Quantification of its σ- and π-Components Using Molecular Tailoring Approach

For a series of tropolones, the nature of the intramolecular O-H⋅⋅⋅O=C hydrogen bond closing the five-membered quasi-cycle was studied. Enhancement of conjugation in the hydrogen-bonded rotamer was revealed. Quantification of hydrogen bond energy in tropolones via the molecular tailoring approach yields values in the range from 15 to 20 kcal/mol suggesting that the intramolecular interaction in tropolones has nature of the resonance-assisted hydrogen bond. The total resonance-assisted hydrogen bond energy in the tropolones was divided into σ- and π-components. The magnitudes of total energy of resonance-assisted hydrogen bond in the substituted tropolones can be controlled by the electronic properties of the substituents at the tropone ring. In 3-, 4-, and 5-substituted tropolones, the resonance-assisted hydrogen bond energy is raised due to electron-donating substituents and lowered due to electron-withdrawing ones. The opposite trend is observed in 7-substituted tropolones. The size of the π-shares plays a crucial role in establishing the total energy of resonance-assisted hydrogen bond. The reason for the occurrence of a resonance-assisted hydrogen bond in the tropolones is the molecular backbone aromaticity, since, in accordance with the Hückel rule, 10 π-electrons are delocalized.

Fluorescence of p-hydroxyazobenzocrowns - Tautomeric equilibrium effect

The spectroscopic properties of a series of para-hydroxyazobenzocrowns, including three novel compounds, were investigated using UV-Vis absorption and emission spectroscopy. This study presents, for the first time, determined quantum yield (QY) values for macrocycles of this category, ranging between 0.122 and 0.195. The highest values were obtained for crowns bearing two phenyl substituents in benzene rings. The impact of aromatic ring substituents and macroring size on the spectral characterization (1H NMR and FTIR) of p-hydroxyazobenzocrowns was examined in consideration of the azophenol ⇄ quinone-hydrazone tautomeric equilibrium. Dipole moments of p-hydroxyazobenzocrowns in the ground and excited states have been determined. The alignment between experimental findings and theoretical studies was established.

Quantification of hydrogen bond energy based on equations using spectroscopic, structural, QTAIM-based, and NBO-based descriptors which calibrated by the molecular tailoring approach

CONTEXT

Hydrogen bonds critically influence the structure and properties of both organic molecules and biomolecules, as well as supramolecular assemblies. For this reason, the development and elaboration of methods for quantitative assessment of hydrogen bond energy is an urgent challenge. In this study, using a large series of hydroxycarbonyl aliphatic compounds with the O‒H···O = C intramolecular hydrogen bond, a bank of hydrogen bond descriptors was created, including spectroscopic, structural, QTAIM-based, and NBO-based parameters. It was shown that the O‒H vibration frequency, OH chemical shift as the spectroscopic descriptors, the O···H hydrogen bond length, O···O distance, and O‒H covalent bond length as the structural descriptors, the electron density and its Laplacian, electron potential energy density in the hydrogen bond critical point, the electron density at the ring critical point as the QTAIM-based descriptors change in a correlated manner. The same correlation is found in change of the charge transfer energy through a hydrogen bond, the occupancy of the O‒H bond antibonding orbital, the Wiberg indices of the O···H hydrogen bond, and the O‒H covalent bond, as well as the polarization of the O‒H bond, which are the NBO-based descriptors. It was also recognized that the specified descriptors from the spectroscopic, structural, QTAIM-based, and NBO-based categories are functionally related to the values of intramolecular hydrogen bond energy, quantified via the molecular tailoring approach. This allowed one to obtain a system of equations for quantitative estimation of intramolecular hydrogen bond energy based on the spectroscopic, structural, QTAIM, and NBO descriptors, which makes such quantification more dependable and reliable.

METHODS

To obtain the spectroscopic descriptors, the vibrational spectra and shielding constants were calculated using the GIAO method. Structural descriptors were obtained for the equilibrium geometry of molecules, calculated at the MP2(FC)/6-311 +  + (2d,2p) level using the Gaussian 09 program. The QTAIM-based descriptors were calculated using the AIMAll program within the framework of the quantum theory "Atoms in Molecules." The NBO-based descriptors were calculated using the NBO 3.1 program implemented into Gaussian 09. To quantify the energy of intramolecular hydrogen bonds, molecular fragmentation was used within the molecular tailoring approach.

Revealing the Reasons for Degeneration of Resonance-Assisted Hydrogen Bond on the Aromatic Platform: Calculations of Ortho-, Meta-, Para-Disubstituted Benzenes, and (Z)-(E)-Olefins

The energies of the O-H∙∙∙O=C intramolecular hydrogen bonds were compared quantitatively for the series of ortho-disubstituted benzenes and Z-isomers of olefins via a molecular tailoring approach. It was established that the hydrogen bond energy in the former series is significantly less than that in the latter one. The reason for lowering the hydrogen bond energy in the ortho-disubstituted benzenes compared to the Z-isomers of olefins is the decrease in the π-contribution to the total energy of the complex interaction, in which the hydrogen bond per se is enhanced by the resonance effect. By the example of the para- and meta-disubstituted benzenes, as well as E-isomers of olefins, it was explicitly shown that the aromatic ring is a much poorer conductor of the resonance effect compared to the double bond. The hydrogen bond in the ortho-disubstituted benzenes has a lower energy than a typical resonance-assisted hydrogen bond because the aromatic moiety cannot properly assist the hydrogen bond with a resonance effect. Thus, a hydrogen bond on an aromatic platform should fall into a special category, namely an aromaticity-assisted hydrogen bond, which is closer by nature to a simple hydrogen bond rather than to a resonance-assisted one.

Common Patterns of Hydrolysis Initiation in P-loop Fold Nucleoside Triphosphatases

The P-loop fold nucleoside triphosphate (NTP) hydrolases (also known as Walker NTPases) function as ATPases, GTPases, and ATP synthases, are often of medical importance, and represent one of the largest and evolutionarily oldest families of enzymes. There is still no consensus on their catalytic mechanism. To clarify this, we performed the first comparative structural analysis of more than 3100 structures of P-loop NTPases that contain bound substrate Mg-NTPs or their analogues. We proceeded on the assumption that structural features common to these P-loop NTPases may be essential for catalysis. Our results are presented in two articles. Here, in the first, we consider the structural elements that stimulate hydrolysis. Upon interaction of P-loop NTPases with their cognate activating partners (RNA/DNA/protein domains), specific stimulatory moieties, usually Arg or Lys residues, are inserted into the catalytic site and initiate the cleavage of gamma phosphate. By analyzing a plethora of structures, we found that the only shared feature was the mechanistic interaction of stimulators with the oxygen atoms of gamma-phosphate group, capable of causing its rotation. One of the oxygen atoms of gamma phosphate coordinates the cofactor Mg ion. The rotation must pull this oxygen atom away from the Mg ion. This rearrangement should affect the properties of the other Mg ligands and may initiate hydrolysis according to the mechanism elaborated in the second article.

Computational 1 H and 13 C NMR in structural and stereochemical studies

Present review outlines the advances and perspectives of computational ¹ H and ¹³ C NMR applied to the stereochemical studies of inorganic, organic, and bioorganic compounds, involving in particular natural products, carbohydrates, and carbonium ions. The first part of the review briefly outlines theoretical background of the modern computational methods applied to the calculation of chemical shifts and spin-spin coupling constants at the DFT and the non-empirical levels. The second part of the review deals with the achievements of the computational ¹ H and ¹³ C NMR in the stereochemical investigation of a variety of inorganic, organic, and bioorganic compounds, providing in an abridged form the material partly discussed by the author in a series of parent reviews. Major attention is focused herewith on the publications of the recent years, which were not reviewed elsewhere.

Guide to tuning the chalcone molecular properties based on the push-pull effect energy scale created via the molecular tailoring approach

Using the molecular tailoring approach, a total energy scale for the push-pull effect in the range from -40 to 100 kcal/mol is created for the wide series of neutral, charged and doubly charged compounds on the chalcone platform. Taking into account similar energy scale for hydrogen bonds, the strength of the push-pull effect is ranked in the seven categories, ranging from negative (anti-push-pull) to very weak and very strong push-pull effect. It is demonstrated that the molecular properties of chalcone can be tuned prior synthesis due to the created energy scale for the push-pull effect. The single bonds of the π-spacer in the chalcones are shortened, the double ones are lengthened, and the C=O bond vibrations are red shifted when the push-pull effect is enhanced along the energy scale. The HOMO and LUMO energies change systematically while the HOMO-LUMO energy gap narrows as the strength of the push-pull effect increases.

New potential application of hydroxypropyl-β-cyclodextrin in solid self-nanoemulsifying drug delivery system and solid dispersion

The purpose of this study was to use hydroxypropyl-β-cyclodextrin (HP-β-CD) as a novel carrier in solid SNEDDS and solid dispersions to enhance the solubility and oral bioavailability of poorly water-soluble dexibuprofen. The novel dexibuprofen-loaded solid SNEDDS was composed of dexibuprofen, corn oil, polysorbate 80, Cremophor® EL, and HP-β-CD at a weight ratio of 45/35/50/15/100. This solid SNEDDS spontaneously formed a nano-emulsion with a size of approximately 120 nm. Unlike the conventional solid SNEDDS prepared with colloidal silica as a carrier, this dexibuprofen-loaded solid SNEDDS exhibited a spherical structure. Similar to the dexibuprofen-loaded solid dispersion prepared with HP-β-CD, the transformation of the crystalline drug to an amorphous state with no molecular interactions were observed in the solid SNEDDS. Compared to the solid dispersion and dexibuprofen powder, solid SNEDDS significantly enhanced drug solubility and AUC. Therefore, HP-β-CD is a novel potential carrier in SNEDDS for improving the oral bioavailability of dexibuprofen.

Facile fabrication of WS2 nanocrystals confined in chlorella-derived N, P co-doped bio-carbon for sodium-ion batteries with ultra-long lifespan

Sodium-ion batteries (SIBs) have been regarded as a promising substitute for lithium-ion batteries but there are still formidable challenges in developing an anode material with adequate lifespan and outstanding rate performance. Transition metal dichalcogenides (TMDs) are promising anode materials for SIBs due to their high theoretical capacities. However, their severe volume expansions and low electronic conductivity impede their practical developments. In addition, the synthesis of energy storage materials from waste biomass has aroused extensive attention. Herein, we synthesize WS₂ nanocrystals embedded in N and P co-doped biochar via a facile bio-sorption followed by sulphurization, employing waste chlorella as the adsorbent and bio-reactor. The WS₂ nanocrystals are beneficial for storing more sodium ions and expediting the transportation of sodium ions, thus improving the capacity and reaction kinetics. Chlorella acts as a reactor and not only inhibits the stacking of WS₂ nanocrystals during the synthesis process but also alleviates the mechanical pressure of composite during the charge/discharge process. As a result, the WS₂/NPC-2 electrode delivers a high specific capacity (436 mA h g^-1 at 0.1 A g^-1) and superior rate performance of 311 mA h g^-1 at 3 A g^-1 for SIBs. It also exhibits excellent stability even up to 6000 cycles at 5 A g^-1, which is one of the optimal long-cycle properties reported for WS₂-based materials to date.

A composite of ultra-fine few-layer MoS2 structures embedded on N,P-co-doped bio-carbon for high-performance sodium-ion batteries

Highly dispersed ultra-fine few-layer MoS₂ embedded on N/P co-doped bio-carbon composite (MoS₂-N/P-C) was synthesized and it delivers excellent high-rate long term cycling performance (175 mA h g⁻¹ after 2000 cycles at 5 A g⁻¹).

A molecular tailoring approach – a new guide to quantify the energy of push–pull effects: a case study on (E)-3-(1H-pyrrol-2-yl)prop-2-enones

We report a new approach to quantify the push–pull effect in molecules with internal charge transfer.

2H-Indazole Tautomers Stabilized by Intra- and Intermolecular Hydrogen Bonds

2-[(2H-Indazol-3-yl)methylene]-1H-indene-1,3(2H)-dione 6 and (E)-2-[(2H-indazol-3-yl)methylene]-2,3-dihydro-1H-inden-1-one 7 have been synthesized. In the crystal, the NH hydrogen atom of 6 is disordered between the N(1) and N(2) atoms with the population ratio of 0.69:0.31. Molecule 7 crystallizes in two tautomeric polymorphs: 7-1H tautomer (yellow) and 7-2H tautomer (red). Both 6 and 7 form centrosymmetric dimers in the crystal with the monomeric units linked by C═O···H···N bifurcated hydrogen bonds in 6 and N-H···N hydrogen bonds in 7. According to ¹H and ¹³C NMR data, in DMSO-d₆ solution, the 6-1H tautomer predominates, whereas in less polar CDCl₃ or CD₂Cl₂, the 6-2H tautomer is stabilized by a strong N-H···O═C intramolecular hydrogen bond. Compound 7 in dimethyl sulfoxide (DMSO) or ethanol solutions exists in the form of 7-1H and 7-2H tautomers. On the example of the 7-2H tautomer, it was shown for the first time that the 2H tautomers of 3-substituted indazoles can be stabilized by an intermolecular hydrogen bond and may remain in aprotic solvents almost indefinitely. However, in the open air or in water, fast 2H → 1H tautomerization occurs. As follows from density functional theory calculations, the high stability of the 2H form in solution is due to the formation of centrosymmetric dimers, which are more stable than the corresponding dimers of the 1H tautomer.

Assessing Parameter Suitability for the Strength Evaluation of Intramolecular Resonance Assisted Hydrogen Bonding in o-Carbonyl Hydroquinones

Intramolecular hydrogen bond (IMHB) interactions have attracted considerable attention due to their central role in molecular structure, chemical reactivity, and interactions of biologically active molecules. Precise correlations of the strength of IMHB's with experimental parameters are a key goal in order to model compounds for drug discovery. In this work, we carry out an experimental (NMR) and theoretical (DFT) study of the IMHB in a series of structurally similar o-carbonyl hydroquinones. Geometrical parameters, as well as Natural Bond Orbital (NBO) and Quantum Theory of Atoms in Molecules (QTAIM) parameters for IMHB were compared with experimental NMR data. Three DFT functionals were employed to calculated theoretical parameters: B3LYP, M06-2X, and ωB97XD. O…H distance is the most suitable geometrical parameter to distinguish among similar IMHBs. Second order stabilization energies ΔEij(2) from NBO analysis and hydrogen bond energy (EHB) obtained from QTAIM analysis also properly distinguishes the order in strength of the studied IMHB. ΔEij(2) from NBO give values for the IMHB below 30 kcal/mol, while EHB from QTAIM analysis give values above 30 kcal/mol. In all cases, the calculated parameters using ωB97XD give the best correlations with experimental ¹H-NMR chemical shifts for the IMHB, with R² values around 0.89. Although the results show that these parameters correctly reflect the strength of the IMHB, when the weakest one is removed from the analysis, arguing experimental considerations, correlations improve significantly to values around 0.95 for R².

Theoretical calculations of carbon-hydrogen spin-spin coupling constants

Structural applications of theoretical calculations of carbon-hydrogen spin-spin coupling constants are reviewed covering papers published mainly during the last 10-15 years with a special emphasis on the most notable studies of hybridization, substitution and stereoelectronic effects together with the investigation of hydrogen bonding and intermolecular interactions. The wide scope of different applications of calculated carbon-hydrogen couplings in the structural elucidation of particular classes of organic and bioorganic molecules is reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives, as well as on natural compounds and carbohydrates. The review is dedicated to Professor Emeritus Michael Barfield in view of his invaluable pioneering contribution to this field.