Atom Lone Pair Research Articles

Novel Trifunctional Intramolecular Frustrated Lewis Pair Derived From Aminoboronic Acid for Converting CO2 Into Valuable Chemicals

ABSTRACTThe conversion of CO2 into valuable chemicals remains a significant challenge for achieving environmental sustainability, primarily due to the stability of the CO2 molecule. This necessitates the development of efficient and ecofriendly catalysts. In recent years, frustrated Lewis pairs (FLPs) have shown promise for CO2 utilization. In this study, we introduce α‐aminodiboronic acid (DBA), a novel trifunctional aminoboronic acid, as an intramolecular FLP for converting CO2 into cyclic carbonate and formic acid. Using density functional theory (DFT) calculations, we explored the reaction mechanism and investigated DBA's electronic structure through molecular electrostatic potential surface (MESP) and natural bond orbital (NBO) analyses. Our results reveal that one −B (OH)2 group induces an unusual state of frustration in the molecule due to charge transfer from the nitrogen atom's lone pair to the π* orbitals, enhancing catalytic performance. The additional −B (OH)2 group serves as an anchoring site for reactive species. The epoxide activation energy is reduced by approximately 27 kcal/mol compared to the uncatalyzed reaction, and the reduction of CO2 occurs with a requirement of 26 kcal/mol. The additional −B (OH)2 plays a crucial role in the catalytic mechanism and minimizes the energies of various structures observed in the reaction path. The reaction energetics align with structural analysis observations, marking this study as the first report on single‐molecule trifunctional FLPs for transforming CO2 into valuable chemicals.

Triazoles in Medicinal Chemistry: Physicochemical Properties, Bioisosterism, and Application.

Triazole demonstrates distinctive physicochemical properties, characterized by weak basicity, various dipole moments, and significant dual hydrogen bond acceptor and donor capabilities. These features are poised to play a pivotal role in drug-target interactions. The inherent polarity of triazole contributes to its lower logP, suggesting the potential improvement in water solubility. The metabolic stability of triazole adds additional value to drug discovery. Moreover, the metal-binding capacity of the nitrogen atom lone pair electrons of triazole has broad applications in the development of metal chelators and antifungal agents. This Perspective aims to underscore the unique physicochemical attributes of triazole and its application. A comparative analysis involving triazole isomers and other heterocycles provides guiding insights for the subsequent design of triazoles, with the hope of offering valuable considerations for designing other heterocycles in medicinal chemistry.

Microscopic solvent-solute interactions, reactivity studies, structure properties and anti cancer activity of 1-(1-benzofuran-5-yl)-N-methylbutan-2-amine

Cancer continues to be a major threat to mankind, as seen by the 19.3 million people who received treatment for the disease in 2020. The study employed quantum mechanical calculations utilising (DFT) B3LYP, using a 6–311++ G(d,p) basis set, to analyse structural characteristics and intramolecular interactions and pharmaceutical aspect of anti-cancer. The study utilised various spectroscopy techniques, including FT-IR, FT-Raman and UV–Vis to examine the molecular arrangements of 1-(1-benzofuran-5-yl)-N-methylbutan-2-amine (1BF5MB).Significant interactions were seen because of the electron-density shift of nitrogen atom's lone pair (LP (O1)) to its antibonding orbital (σ ∗ ) (C13-H30), with an E(2) of 8.51 Kcal/mol. This indicates a substantial degree of electron delocalization. TDM analysis displays graphs that illustrate the capacity to transmit charges. ALIE analysis utilises the colour blue to represent the stable sigma bonds, namely those associated with hydrogen atoms that produce protons. Evaluating the drug-likeness and ADMET assessment enabled the biological features of (1BF5MB). This compound may be deemed a strong anti-tubercular treatment agent due to its relatively low binding affinities for the specific receptors.These results indicate that the drugs block these receptors.

Theoretical Evaluation of Eco-friendly Designed Nonionic Sugar-based Surfactants

Abstract: This study deals with the density functional theory calculations of eco-friendly designed nonionic sugar-based surfactants (SurfRing and SurfLinear). Then, it compares the results with the structural and electronic properties of a fatty alcohol surfactant (SurfFA). All geometry optimizations and energy calculations were performed using M06-2X functional and 6-31G(d,p) basis sets. The quantum chemistry reactivity parameters showed the effect of hydrophilic fragment structure on intramolecular interactions and conformational stability of surfactants. The results showed that SurfRing is more reactive than SurfFA. Based on Bader’s quantum theory of atoms in molecules (QTAIM), one intramolecular hydrogen bond (O43…H67―O57, EHB: -11.9 kcal.mol-1) is characterized for SurfRing, while two hydrogen bond interactions (O63…H60―O59 and O65…H64―O63 with EHB of -13.0, and -12.3 kcal.mol-1, respectively) form between the hydroxyl groups of SurfLinear. These intramolecular hydrogen bonds are partially covalent interactions. Natural bond orbital analysis reveals that the most prominent interaction energy is electron donation from the oxygen atom lone pair to the antibonding orbital of the O―H bond supporting the results obtained from the AIM calculations.

A Model Halogen-Bonded Network as a Potential Tube-like Host for Li+: A DFT Study

The formation of a halogen-bonded network using four NHX-(CH2)3-NX-(CH2)3-NHX molecules (X = Cl, Br, or I) is investigated using DFT. The self-assembly of the four basic motifs results in a tube-like structure with C4h symmetry, with one halogen-bonded network located at each end of the structure and one at its center. Each halogen-bonded network has four quasi-planar N-X···N interactions with binding energies that increase with the size of X. The structure is found to bind Li+ at each of the halogen-bonded networks, albeit more strongly at its center. The binding of Li+ is driven by halogen atom lone pairs that produce a rich electron density orthogonal to the halogen bond. The presence and strength of the interactions are further examined using AIM and NBO calculations. Lastly, IRC calculations are performed to examine the transitions between the Li+ complex minima and, thus, the potential for transporting the metal ion from one end of the tube to the other. Based on the tetrameric structure, a model intramolecular structure is built and considered as a potential host for Li+. In this case, the central intermolecular N-X···N network is replaced by an intramolecular Si-C≡C-Si network. Interestingly, both intermolecular and intramolecular structures exhibit similar Li+ binding abilities.

DFT-Based Study of the Intramolecular Interactions of Some Aminoglycosides

The quantum chemical modeling and full geometry optimization of sisomicin and gentamicin were carried out by the correlation functional B3LYP using augmented with polarization functions for heavy atoms 6-311G(d) and Dunning’s correlation consistent cc-pVDZ basis sets. The effect of the basis set on the calculation results of molecular structure and quantum chemical descriptors of the titled compounds was studied. Special attention was paid to the intramolecular NH…N, OH…N, OH…O, NH…O hydrogen bonds in sisomicin and gentamicin. According to theoretical calculations, the distances between hydrogen and acceptor atoms are a bit longer than a typical length due to a significant deviation of the intramolecular H-bonds from a linearity. To evaluate the extent of electron density delocalization from the lone pairs of atoms into the antibonding neighboring orbitals and inside H-bonds within the systems, NBO (Natural Bond Orbital) analysis was used at two levels of theory. The most intensive interactions between electron donor and electron acceptor in the structures under consideration are determined and their delocalization energies are evaluated. Based on the obtained data, classical electrostatic nature of the weak H-bonds and conjugation effects stabilizing the molecules are suggested.

Pnictogen-Bridged Diphenyl Sulfones as Photoinduced Pnictogen Bond Forming Emission Motifs.

In this study, pnictogen (Pn)-bridged diphenyl sulfones were synthesized as motifs for photoinduced dynamic rearrangement. The newly synthesized sulfones exhibited dual fluorescence at 298 K. Density functional theory calculations revealed that the longer-wavelength fluorescence was derived from the geometries after structural relaxation through photo-driven pnictogen bond formation between the O atom lone pair of the sulfonyl moiety and the antibonding orbital of the Pn-C bond. This is the first report on emission dynamics driven by pnictogen bond formation upon photoexcitation.

Extra-long C[sbnd]C single bonds via negative hyperconjugation in perfluoropinacolate complexes

A computational study on a series of pinacolate ligands with varying degrees of fluorination (from four to zero CF3 groups) has been carried out to understand the exceptionally long central CC bonds in crystal structures with the perfluoropinacolate ligand, (pinF). The systems were studied with both DFT (PBE0) and ab-initio (MP2 NEVPT2) models to elucidate the features of the electronic structure responsible for the elongated central bond routinely observed in {A(pinF)} species. Two main influences are responsible: (i) negative hyperconjugation exists between the alkoxide O atom lone pairs and the central CC σ* bond which also have resonance forms that formally break the central CC bond and (ii) the lack of hydrogen bonding between any CH bonds and the ligand O atoms. Steric influences do not play a significant role, but a central atom A with a point charge of at least plus two bound to pinF is required to reproduce the crystallographically determined CC distances.

Revealing the Role of the Cyaphide Ion as a Bridging Ligand in Heterometallic Complexes.

The synthesis of heterometallic transition metal complexes featuring bridging cyaphide ions (C≡P−) is reported. These are synthesized from reactions of Au(IDipp)(CP) (IDipp=1,3‐bis(2,6‐diisopropylphenyl)imidazol‐2‐ylidene) with electron‐rich, nucleophilic transition metal reagents, affording Au(IDipp)(μ2−C≡P)Ni(MeI i Pr)2 (MeI i Pr=1,3‐diisopropyl‐4,5‐dimethylimidazol‐2‐ylidene) and Au(IDipp)(μ2−C≡P)Rh(Cp*)(PMe3). These studies reveal that, in contrast to the cyanide ion, bimetallic cyaphido complexes strongly favor a η1 : η2 coordination mode that maximizes the interaction of the second metal (Ni, Rh) with the π‐manifold of the ion (and not the phosphorus atom lone pair). End‐on bridging can be effectively unlocked by blocking the π‐manifold, as demonstrated by reaction of Au(IDipp)(μ2−C≡P)Rh(Cp*)(PMe3) with an electrophilic transition metal reagent, W(CO)5(THF), which affords the heterotrimetallic compound Au(IDipp)(μ3−C≡P)[Rh(Cp*)(PMe3)][W(CO)5].

Revealing the Role of the Cyaphide Ion as a Bridging Ligand in Heterometallic Complexes

AbstractThe synthesis of heterometallic transition metal complexes featuring bridging cyaphide ions (C≡P−) is reported. These are synthesized from reactions of Au(IDipp)(CP) (IDipp=1,3‐bis(2,6‐diisopropylphenyl)imidazol‐2‐ylidene) with electron‐rich, nucleophilic transition metal reagents, affording Au(IDipp)(μ2−C≡P)Ni(MeIiPr)2 (MeIiPr=1,3‐diisopropyl‐4,5‐dimethylimidazol‐2‐ylidene) and Au(IDipp)(μ2−C≡P)Rh(Cp*)(PMe3). These studies reveal that, in contrast to the cyanide ion, bimetallic cyaphido complexes strongly favor a η1 : η2 coordination mode that maximizes the interaction of the second metal (Ni, Rh) with the π‐manifold of the ion (and not the phosphorus atom lone pair). End‐on bridging can be effectively unlocked by blocking the π‐manifold, as demonstrated by reaction of Au(IDipp)(μ2−C≡P)Rh(Cp*)(PMe3) with an electrophilic transition metal reagent, W(CO)5(THF), which affords the heterotrimetallic compound Au(IDipp)(μ3−C≡P)[Rh(Cp*)(PMe3)][W(CO)5].

Characterizing the n→π* interaction of pyridine with small ketones: a rotational study of pyridine⋯acetone and pyridine⋯2-butanone.

Complexes formed by pyridine and small ketones such as acetone and 2-butanone have been generated in a supersonic jet and characterized by broadband Fourier transform microwave spectroscopy combined with high-level theoretical computations. The spectra of the complexes show a quadrupole coupling hyperfine structure due to the presence of a nitrogen atom and the splittings owing to the low barriers of the internal rotation of the methyl groups bonded to the carbonyl group. The corresponding barriers have been determined from the analysis of the spectra. We show in both complexes that pyridine closes a cycle with a ketone carbonyl group through an N⋯CO n→π* tetrel interaction and a C-H⋯O contact. The n→π* tetrel bond involves the pyridine N atom lone pair and the ketone carbonyl group with a geometry approaching the Bürgi-Dunitz trajectory for the nucleophilic attack to a carbonyl group.

Chalcogen Bonds in Small-Organic Molecule Compounds Derived from the Cambridge Structural Database (CSD)

Growing interest in non-covalent interactions involving chalcogen atoms has been ascribed to their importance in crystal engineering, molecular recognition and macromolecular edifices. The present study is dealing with chalcogen bonds involving divalent Sulphur, Selenium and Tellurium atoms, acting as sigma-hole donors, in small-molecule compounds using the Cambridge Structural Database (CSD) in conjunction with ab initio calculations. Results derived from CSD surveys and computational study revealed that nucleophiles formed complexes with the chalcogen-bond donors R1-X-R2 (X = S, Se or Te). The main forces stabilizing the complexes were chalcogen bonds, enhanced by dispersion interactions. Complexation pattern and energetics show that nucleophile bonding at divalent S, Se and Te atoms is a relatively strong and directed interaction. The bond consists of a charge transfer from a nucleophile atom lone pair to an X-R1 or X-R2 antibonding orbital.

An ab initio study of some hydrogen-bonded complexes of chloroform and bromoform: red-shifted or blue-shifted hydrogen bonds?

The properties of the hydrogen-bonded complexes of chloroform and bromoform with ammonia, water, hydrogen fluoride, phosphine, hydrogen sulphide and hydrogen chloride were studied by means of ab initio calculations. The properties of interest were the molecular structures, the interaction energies, the vibrational spectra and the nature of the orbital interactions involved in the formation of the complexes. Of particular interest was the determination of whether the various interactions exhibited red-shifted or blue-shifted hydrogen bond behaviour. The complexes optimized in three distinct structural models, singly bonded, cyclic and cage. The interaction energies, in the main, varied systematically with changes of the haloform and of the partner molecules. Changes of the CH or YH (Y = N, O, F, P, S and Cl) bond lengths correlated in most cases with the interaction energies, subject to some inconsistencies, with opposite behaviour being shown by the two sets. Similarly, the CH and YH stretching wavenumber shifts also displayed a dependence on the interaction energies, tracking with the bond length changes. Based on the diagnostic utility of these structural and spectroscopic properties, the complexes were found to be almost exclusively red-shifted, for binding through both the CH and YH groups. The orbital interactions responsible for the stability of the complexes were determined to be donation from a Y atom lone pair orbital of the partner molecule to a CH σ antibonding orbital and from a X lone pair orbital (X = Cl and Br) of the haloform to a YH σ antibonding orbital.

An electron localization function analysis of the molecular mechanism and the C–O bond formation in the [3+2] cycloaddition reaction involving zwitterionic type between a nitrone and an electron deficient ethyne

The mechanistic nature of a [3+2] cycloaddition reaction involving zwitterionic species has been investigated, and the changes of electron density related to the O–C and C–C bond formation along the intrinsic reaction coordinate have been characterized. This polar [3+2] cycloaddition reaction, which takes place through a non-concerted two-stage one-step mechanism, proceeds with a moderate Gibbs free activation energy of 21 kcal mol−1. The reaction begins by the creation of a pseudoradical centre at the central carbon, first on the dimethyl acetylenedicarboxylate, and second on the nitrone framework. This immediately favours the formation of the first O–C single bond by donation of some electron density of the oxygen atom lone pairs, which represents the most attractive centre in this cycloaddition reaction.

Co-crystals of an organic triselenocyanate with ditopic Lewis bases: recurrent chalcogen bond interactions motifs.

Organic selenocyanates R-Se-CN can act as an amphoteric chalcogen bond (ChB) donor (through the Se atom) and acceptor (through the N atom lone pair). Co-crystallization of tri-substituted 1,3,5-tris(selenocyanatomethyl)-2,4,6-trimethylbenzene (1) is investigated with different ditopic Lewis bases acting as chalcogen bond (ChB) acceptors to investigate the outcome of the competition, as ChB acceptor, between the nitrogen lone pair of the SeCN group and other Lewis bases involving pyridinyl or carbonyl functions. In the presence of tetramethylpyrazine (TMP), benzoquinone (BQ) and para-dinitrobenzene (pDNB) as ditopic Lewis bases, a recurrent oligomeric motif stabilized by six ChB interactions is observed, involving six SeCN groups and the ChB acceptor sites of TMP, BQ and pDNB in the 2:1 adducts (1)2·TMP, (1)2·BQ and (1)2·pDNB.

Halogen bonding in self-assembling systems: A comparison of intra- and interchain binding energies

Calculations using the M06-2X and ωB97-XD density functionals with a triple-zeta quality polarized basis sets have been used to investigate the binding energies in a series of halogen bonded complexes of C2F4I2 with NC(CH2)nCN (n = 0–2). Results for complexes with monomer ratios from 1:1 to 3:3 indicate a near constant binding energies per halogen bond of ∼8 kJ/mol, ∼13 kJ/mol, and ∼14 kJ/mol for n = 0–2, respectively, indicating no observable cooperative effects in the linear halogen bonding. Results from calculations on the stacking energy of the linear chains for systems up to 3:3 indicated that these binding energies were comparable to those for the linear halogen bonds. The strong stacking interaction is hypothesized to be due to favorable electrostatic forces between the F atoms on C2F4I2 with either adjacent H atoms on NC(CH2)2CN, or the CC π-hole on NCCN. The stacking interactions showed a significant cooperative effect, as well as a synergistic effect with the linear halogen bonds as demonstrated by a shortening of the I⋯N distances in the component chains. Binding energies for all 1:1 complexes of C2F4I2 and C4F8I2 with NC(CH2)nCN (n = 0–4) show a strong linear correlation with the ΔESP between the positive σ-hole on the I atom and the negative region around the N atom lone pair.

The Anomeric Effect: It's Complicated.

The origin of the anomeric effect has been reexamined in a coordinated experimental and computational investigation. The results of these studies implicate a number of different, but correlated, interactions that in the aggregate are responsible for the anomeric effect. No single factor is uniquely responsible for the axial preference of a substituent that is the hallmark of the anomeric effect. A CH···G nonbonded attraction between a polar axial substituent (G) and the syn-axial hydrogen(s) in the heterocycle has been demonstrated experimentally. The hyperconjugation model involving electron transfer from a ring heteroatom to an excited state of an axial C-G bond was shown to be, at most, a minor contributor because of the very small changes in charge density at the ring heteroatom(s): the main charge transfer is from hydrogen to G in the H-C-G unit. This appears to result from lengthening the C-G bond to minimize repulsion with the ring atom lone pair(s) and the advantage of having a more positive hydrogen that leads to a stabilizing Coulombic interaction with the ring heteroatom(s). In short, the anomeric effect arises mainly from two separate CH···G nonbonded Coulombic attractions.

Assignment of photoelectron spectra of intramolecular silicon complexes: 1-vinyl- and 1-phenylsilatranes.

The problematic experimental photoelectron spectra of silatranes XSi[OCH2CH2]3N (X = vinyl and Ph) were theoretically studied. The ab initio electron propagator theory, many-body methods, and model vibrational Hamiltonian were employed to establish the nature of bands in the energetically lowest part of the photoelectron spectrum of these intramolecular silicon complexes. The first vertical ionization energy corresponds to a nitrogen atom lone pair, nN, in 1-vinylsilatrane, and the essentially doubly degenerate π-orbitals πPh and πPh' of the aromatic ring in 1-phenylsilatrane. Peaks at 9.6 and 9.9 eV in the spectra of both compounds, previously associated with the removal of an electron from the lone pair level of the equatorial oxygens, should actually be assigned to the bonding orbital HV1 of their 3c-4e axial CSi←N moiety. Taking silatranes with X = H, Me, OEt, F, vinyl, and Ph as examples, it was found that the length of the dative Si←N contact and the ionization energy of HV2 (formally nN) were in a good linear relationship. Regardless of the nature of the X substituent, this relationship could be used for the identification of orbitals that participate in the formation of the coordination Si←N bond in the wide series of XSi[OCH2CH2]3N and their structural analogs.

NMR Chemical Shift of a Helium Atom as a Probe for Electronic Structure of FH, F-, (FHF)-, and FH2.

In this work, we present the first results of outer electronic shell visualization by using a 3He atom as a probe particle. As model objects we have chosen F-, FH, and FH2+ species, as well as the hydrogen-bonded complex FH···F- at various H···F- distances (3.0, 2.5, 2.0, and 1.5 Å and equilibrium at ca. 1.14 Å). The interaction energy of investigated objects with helium atom (CCSD/aug-cc-pVTZ) and helium atom chemical shift (B3LYP/pcS-2) surfaces were calculated, and their topological analysis was performed. For comparison, the results of standard quantum mechanical approaches to electronic shell visualization were presented (ESP, ELF, ED, ∇2ED). We show that the Laplacian of helium chemical shift, ∇2δHe, is sensitive to fluorine atom lone pair localization regions, and it can be used for the visualization of the outer electronic shell, which could be used to evaluate the proton accepting ability. The sensitivity of ∇2δHe to lone pairs is preserved at distances as large as 2.0-2.5 Å from the fluorine nucleus (in comparison with the distance to ESP minima, located at 1.0-1.5 Å or maxima of ELF, which are as close as 0.6 Å to the fluorine nucleus).

Structure and Dynamics in Formamide-(H2O)3: A Water Pentamer Analogue.

Water self-association dominates the formation of microsolvated molecular clusters which may give rise to complex structures resembling those of pure water clusters. We present a rotational study of the complex formamide-(H2O)3 formed in a supersonic jet and several monosubstituted isotopologues. Formamide and water molecules form a four-body sequential cycle through N-H···O, O-H···O, and O-H···O═C hydrogen bonds, resulting in a chiral structure with a nonplanar skeleton that can be overlapped to that of water pentamer. The analysis of the 14N-nucleus quadrupole coupling effects shows the depletion of the electron density of the N atom lone pair with respect to the bare formamide that affects the amide group C-N and C═O distances. The study of the observed tunneling doublets shows that formamide-(H2O)3 follows a path to invert its structure driven by the flipping of water subunits and passing through successive nonplanar configurations, a motion reminiscent of the pseudorotation of water pentamer.