Unravelling performance of honeycomb structures as drug delivery systems for the isoniazid drug using DFT-D3 correction dispersion and molecular dynamic simulations

In this study, the potential of aluminum nitride (h-AlN), boron nitride (h-BN) and silicon carbide (h-SiC) nanosheets as the drug delivery systems (DDS) of isoniazid (INH) was scrutinized through density functional theory (DFT) and molecular dynamic (MD) simulations. We performed DFT periodic calculations on the geometry and electronic features of nanosheets adsorbed with INH by the DFT functional (DZP/GGA-PBE) employed in the SIESTA code. In the energetically favorable model, an oxygen atom of the C-O group of the INH molecule interacts with a Si atom of the h-SiC at 2.077 Å with an interaction energy of -1.361 eV. Charge transfer (CT) calculation by employing the Mulliken, Hirshfeld and Voronoi approaches reveals that the monolayers and drug molecules act as donors and acceptors, respectively. The density of states (DOS) calculations indicate that the HOMO-LUMO energy gap (HLG) of the h-SiC nanosheet declines significantly from 2.543 to 1.492 eV upon the adsorption of the INH molecule, which causes an electrical conductivity increase and then produces an electrical signal. The signal is linked to the existence of INH, demonstrating that h-SiC may be an appropriate sensor for INH sensing. The decrease in HLG for the interaction of INH and h-SiC is the uppermost (up to 41%) representing the uppermost sensitivity, whereas the sensitivity trend is σ(h-SiC) > σ(h-AlN) > σ(h-BN). Quantum theory of atoms in molecules (QTAIM) investigations is employed to scrutinize the nature of the INH/nanosheet interactions. The QTAIM analysis reveals that the interaction of the INH molecule and h-SiC has a partially covalent nature, while INH/h-AlN model electrostatic interaction occurs in the system and noncovalent and electrostatic interaction for the INH/h-BN model. Finally, the state-of-the-art DFT-MD simulations utilized in this study can mimic ambient conditions. The results obtained from the MD simulation show that it takes more time to bond the INH drug and h-SiC, and the INH/h-SiC system becomes stable. The results of the current research demonstrate the potential of h-SiC as a suitable sensor and drug delivery platform for INH drugs to remedy tuberculosis.

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.

Towards the critical understanding of selected vibrational features in biologically important dicyano aromatic conjugated molecules: Importance of electron donating/withdrawal groups and geometry associated with dicyano group

The Raman spectra of a series of synthesized DC molecules (benzylidene malononitrile derivatives) with different electron donating (EDG) and electron withdrawing (EWG) group have been presented and analyzed with DFT calculated spectra. In particular, different functional groups effect on cyano stretching (∼2200 cm^-1), phenyl ring breathing and alkenic double bond stretch which often appears mixed up (1475-1650 cm^-1) are studied systematically for several aromatic conjugated DC derivatives. Interestingly, symmetric stretching frequency of the DC compounds having two CN groups at geminal position appears at higher wavenumber (by 11-15 cm^-1) compared to their corresponding asymmetric stretch frequency. Angle (between dicyano group) dependent theoretical study indicates that the relative appearance of cyano symmetric/anti-symmetric stretching frequency depends on whether dicyano groups are at the geminal or vicinal position and the angle between them. Complete band assignments of observed Raman frequencies have been performed by potential energy distributions (PEDs) available in GAR2PED software. Our results will help to understand the vibrational feature of this important class of compounds in biological medium when used as probe.

Important role of the position of a functional group in isomers for photophysical and antibacterial properties: a case study with naphthalenemaleonitrile positional isomers

The position of the functional group alters the interactions in the crystal packing, thereby altering the fluorescence responses as well as the antibacterial activities.

π-Hydrogen bonding and aromaticity: a systematic interplay study

Quantum DFT calculations, corrected for long-range interactions, have been carried out on complex models formed between HF as a proton donor and 2-methylene-2H-indene derivatives as proton acceptors. Using various exocyclic X substitutions, mutual effects of the aromaticity and the strength of the resulting π-hydrogen bond (after its evaluation by AIM methodology) have been investigated. The results show that the aromaticity of 6-membered rings and the hydrogen bond strength increase upon increasing the electron-donating character of the X-substituents. Based on some aromaticity indices (HOMA, FLU, SA and NICS(1)zz), it has been shown that the formation of a π-hydrogen bond causes an increase of aromaticity of the 6-membered ring. Also, the strength of the resulting π-hydrogen bond (with an energy of about 4.0 to 7.0 kcal mol-1) depends on the aromaticity of the 6-membered ring and increases with an increase in the aromaticity. In addition, a linear relationship was found between the most negative value of the molecular electrostatic potential (Vmin) and the HOMA, which confirms that the Vmin in the region of the studied ring could be used as a new index to estimate the amount of aromaticity. The electronic properties of the complexes have also been evaluated by means of the molecular electrostatic potential (MEP), the atoms in molecules (AIM) and the natural bond orbital (NBO) analyses.

Tetrel Bond between 6-OTX₃-Fulvene and NH₃: Substituents and Aromaticity

Carbon bonding is a weak interaction, particularly when a neutral molecule acts as an electron donor. Thus, there is an interesting question of how to enhance carbon bonding. In this paper, we found that the –OCH₃ group at the exocyclic carbon of fulvene can form a moderate carbon bond with NH₃ with an interaction energy of about −10 kJ/mol. The –OSiH₃ group engages in a stronger tetrel bond than does the –OGeH₃ group, while a reverse result is found for both –OSiF₃ and –OGeF₃ groups. The abnormal order in the former is mainly due to the stronger orbital interaction in the –OSiH₃ complex, which has a larger deformation energy. The cyano groups adjoined to the fulvene ring not only cause a change in the interaction type, from vdW interactions in the unsubstituted system of –OCF₃ to carbon bonding, but also greatly strengthen tetrel bonding. The formation of tetrel bonding has an enhancing effect on the aromaticity of the fulvene ring.

Nature of Intramolecular Resonance Assisted Hydrogen Bonding in Malonaldehyde and Its Saturated Analogue

The nature of resonance-assisted hydrogen bonds (RAHB) is still subject of an ongoing debate. We therefore analyzed the σ and π charge redistributions associated with the formation of intramolecular hydrogen bonds in malonaldehyde (MA) and its saturated analogue 3-hydroxypropanal (3-OH) and addressed the question whether there is a resonance assistance phenomenon in the sense of a synergistic interplay between the σ and π electron systems. Our quantum chemical calculations at the BP86/TZ2P level of theory show that the π charge flow is indeed in line with the Lewis structure as proposed by the RAHB model. This typical rearrangement of charge is only present in the unsaturated system, and not in its saturated analogue. Resonance in the π electron system assists the intramolecular hydrogen bond by reducing the hydrogen bond distance, and by providing an additional stabilizing component to the net bonding energy. The σ orbital interaction plays an important role in the enhanced hydrogen bond strength in MA as well. However, there is no resonance assistance in the sense of an interplay between σ charge transfer and π polarization; σ and π contribute independently from each other.

Resonance-assisted stabilisation of hydrogen bonds probed by NMR spectroscopy and path integral molecular dynamics

Path integral molecular dynamics and experimental NMR data are used to investigate resonance-assisted hydrogen bonds (RAHBs). When nuclear delocalisation is included in chemical shift calculations, the agreement with experiment is excellent, while static calculations show very poor performance. The results support the concept of RAHB, which has recently been questioned.

On the roles of close shell interactions in the structure of acyl-substituted hydrazones: An experimental and theoretical approach

The 2-(phenyl-hydrazono)-succinic acid dimethyl ester compound was synthesized by reacting phenylhydrazine with dimethylacetylene dicarboxylate at room temperature and characterized by elemental analysis, infrared, Raman, (1)H and (13)C NMR spectroscopies and mass spectrometry. Its solid state structure was determined by X-ray diffraction methods. The X-ray structure determination corroborates that the molecule is present in the crystal as the hydrazone tautomer, probably favored by a strong intramolecular N-H···O=C hydrogen bond occurring between the carbonyl (-C=O) and the hydrazone -C=N-NH- groups. A substantial fragment of the molecular skeleton is planar due to an extended π-bonding delocalization. The topological analysis of the electron densities (Atom in Molecule, AIM) allows characterization of intramolecular N-H···O interaction, that can be classified as a resonant assisted hydrogen bond (RAHB). Moreover, the Natural Bond Orbital population analysis confirms that a strong hyperconjugative lpO1→σ*(N2-H) remote interaction between the C2=O1 and N2-H groups takes place. Periodic system electron density and topological analysis have been applied to characterize the intermolecular interactions in the crystal. Weak intermolecular interactions determine the crystal packing, and the prevalence of non-directional dispersive contributions are inferred on topological grounds. The IR spectrum of the crystalline compound was investigated by means of density functional theory calculations carried out with periodic boundary conditions on the crystal, showing excellent agreement between theory and the experiments. The vibrational assignment is complemented with the analysis of the Raman spectrum.