Electronegative Regions Research Articles

Mechanistic insight into the aggregation ability of anammox microorganisms: Roles of polarity, composition and molecular structure of extracellular polymeric substances

The chemical characteristics of extracellular polymeric substances (EPS) of anammox bacteria (AnAOB) play a crucial role in the rapid enrichment of AnAOB and the stable operation of wastewater anammox processes. To clarify the influential mechanisms of sludge EPS on AnAOB aggregation, multiple parameters, including the polarity distribution, composition, and molecular structure of EPS, were selected, and their quantitative relationship with AnAOB aggregation was analyzed. Compared to typical anaerobic sludge (anaerobic floc and granular sludge), the anammox sludge EPS exhibited higher levels of tryptophan-like substances (44.82–56.52 % vs. 2.57–39.81 %), polysaccharides (40.02–53.49 mg/g VSS vs. 30.22–41.69 mg/g VSS), and protein structural units including α-helices (20.70–23.98 % vs. 16.48–19.32 %), β-sheets (37.43–42.98 % vs. 25.78–36.72 %), and protonated nitrogen (Npr) (0.065–0.122 vs. 0.017–0.061). In contrast, it had lower contents of β-turns (20.95–27.39 % vs. 28.17–39.04 %). These biopolymers were found to originate from different genera of AnAOB. Specifically, the α-helix-rich proteins were mainly derived from Candidatus Kuenenia, whereas the extracellular proteins related to tryptophan and Npr were closely associated with Candidatus Brocadia. Critically, these EPS components could drive anammox aggregation through interactions. Substantial amounts of tryptophan-like substances facilitated the formation of β-sheet structures and the exposure of internal hydrophobic clusters, which benefited the anammox aggregation. Meanwhile, extracellular proteins with high Npr content played a pivotal role in the formation of mixed protein-polysaccharide gel networks with the electronegative regions of polysaccharides, which could be regarded as the key component in the maintenance of anammox sludge stability. These findings provide a comprehensive understanding of the multifaceted roles of EPS in driving anammox aggregation and offer valuable insights into the development of EPS regulation strategies aimed at optimizing the anammox process.

Design strategy of microbially produced semiconductor maquettes of Cu2Se4SnZn8+ crystal alloy for enhanced harmonic generations

During present study, we have attempted to present few nanosized maquettes of a semiconductor alloy which can be designed under the action of microbes to be utilize for their high-tech applications like their nonlinear optical (NLO) applications. All the designed maquettes are studied for their geometrical, optical, electronic transitions and bonding interactions. It was found that inclusion of late transition metals is more effective in tuning them as NLO switches. Also, the last three maquettes presented both electronegative and electropositive regions to display them as non-sized magnets. Their linear polarizability (<α0 > ), first hyper-polarizability (β0) and second order hyperpolarizability (γ0) values were found as: 0.08–11.42 × 10-24, 0.08.71–11.42 × 10-24, 1.42–71.30 × 10-24 esu respectively. These values were significantly higher than the one presented in literature The intention of this investigation was to investigate the NLO properties of Cu2Se4SnZn8+ crystals for future high-tech applications.

Quantum chemical study of the defect laden monolayer boron nitride nanosheets for adsorption of pesticides from wastewater

The accumulation of hazardous pesticides and their residues in –water sources has raised serious concerns to find a suitable way to eliminate them. In this study, the adsorption behavior of monolayer boron nitride (BN) nanosheet with B, N and B+N vacancies towards the cadusafos, chlorantraniliprole, fluazolate and lufenuron pesticides is investigated using the first principle density functional theory. The molecular electrostatic potential maps, the density of states plots and the HOMO-LUMO energy distributions based on optimized geometries were obtained. The theoretical infrared spectra confirmed the post-adsorption structural changes in defect-laden BN nanosheets. The pesticides formed a stable complex with defect laden BN nanosheets in aqueous media with the release of energy in the range of 40–130 kJ mol-1. The molecular electrostatic potential provided evidence for the appearance of the electronegative regions in the pesticides post adsorption. The most profound effect of electronegative regions was in the case of the BN/B+N nanosheet. The bandgap values of the nanosheets decreased after the interaction with pesticides. The HOMO-LUMO analysis showed that the molecular orbitals resided near the vacancy sites and thus played an important role in determining the adsorption interaction. The adsorption interactions were physical in nature, dominated by weak Van der Waals forces. The adsorption behavior of the BN/N nanosheet was best among the studied adsorbates towards pesticides. These findings give an account of how the defects in monolayered BN nanosheets can enhance the adsorption of organic (pesticide) molecules and develop viable adsorbents for wastewater treatment.

New insights on the effect of the hydrolysing agents in the synthesis of pristine fibrous silica zeolite X for enhancement of side chain methylation of toluene: Theoretical and experimental studies

This article aims to clarify the role of hydrolysing agent in the synthesis of a pristine fibrous silica zeolite X (FZX) catalyst using DFT simulation, thermodynamics, and experimental data. FZX was fabricated using various hydrolysing agents such as urea (FZXU), formamide (FZXF) and N, N methylenediacrylamide (FZXN), to perform the side chain methylation of toluene process. It was found that disparity of hydrolysing agents resulted in different degree of silica hydrolysation which eventually altered the each FZX catalyst properties. Based on the chemical reactivity and visualized charge distributions as revealed by the DFT simulations, it was discovered that most electronegative regions located around negatively charged oxygen in hydrolysing agents structure exhibited a higher degree of silica hydrolysation resulted in excellent catalyst behaviour. Higher density of dendrimeric silica fiber in FZXN reduced the coke formation and induced the formation of extra-framework alumina (EFAl) species. The hydrolysing agents also affect the basicity of the decorated FZX catalyst and followed the sequence FZXN > FZXU > FZXF. The FZXN exhibited higher side chain methylation of toluene catalytic activity of 57 % toluene conversion and 49.6 % of styrene and ethylbenzene yield. Furthermore, a thermodynamic analysis was carried out, and it was discovered that the Boudouard reaction was the primary source of carbon deposition during the side chain methylation of toluene.

X-ray diffraction and Density Functional Theory based structural analyses of 2-phenyl-4-(prop-2-yn-1-yl)-1,2,4-triazolone

This study is composed of X-ray diffraction and Density Functional Theory (DFT) based molecular structural analyses of 2-phenyl-4-(prop-2-yn-1-yl)-2,4-dihydro-3H-1,2,4-triazol-3-one (2PPT). Crystal data for C11H9N3O: Monoclinic, space group P21/c (no. 14), a = 7.8975(2) Å, b = 11.6546(4) Å, c = 11.0648(3) Å, β = 105.212(2)°, V = 982.74(5) Å3, Z = 4, T = 296.15 K, μ(MoKα) = 0.091 mm-1, Dcalc = 1.346 g/cm3, 13460 reflections measured (5.174° ≤ 2Θ ≤ 64.72°), 3477 unique (Rint = 0.0314, Rsigma = 0.0298) which were used in all calculations. The final R1 was 0.0470 (I &gt; 2σ(I)) and wR2 was 0.1368 (all data). The experimentally determined data was supported by theoretically optimized calculations processed with the help of Hartree-Fock (HF) technique and Density Functional Theory with the 6-311G(d,p) basis set in the ground state. Geometrical parameters (Bond lengths and angles) as well as spectroscopic (FT-IR, 1H NMR, and 13C NMR) properties of 2PPT molecule has been optimized theoretically and compared with the experimentally obtained results. Hirshfeld surface analysis with 2D fingerprinting plots was used to figure out the possible and most significant intermolecular interactions. The electronic characterizations such as molecular electrostatic potential map (MEP) and Frontier molecular orbital (FMO) energies have been studied by DFT/B3LYP approach. The MEP imparted the detailed information regarding electronegative and electropositive regions across the molecule. The HOMO-LUMO energy gap as high as 5.3601 eV was found to be responsible for the high kinetic stability of the 2PPT.

Spectroscopic (FT-IR, FT-Raman and UV-Vis), computational (ELF, LOL, NBO, HOMO-LUMO, Fukui, MEP) studies and molecular docking on benzodiazepine derivatives- heterocyclic organic arenes

Abstract Benzodiazepines block the activity of nerves in the brain and the central nervous system whenever it is exceeded. The benzodiazepine derivatives such as CZ and OZ have been taken to characterize the molecular structure by spectroscopic and computational (by B3LYP/HSEH1PBE with 6-311++G(d,p) basis set) methods to obtain chemical, electronic and biological properties. The structures CZ and OZ have been optimized and complete vibrational assignments have been obtained. The transparency and the electronic transitions have been analyzed by UV-Vis spectrum. The maximum wavelength and band gap value obtained by UV-Vis analysis have been compared with HOMO-LUMO values due to delocalization of electrons. Chemical bonding by ELF and LOL, inter and intra-fragments interactions have been explained by scatter graph. Furthermore, acceptor and donor orbitals and nucleophilic and electrophilic interactions were explained using NBO and Fukui analyses. Chemically reactive site has been shown by MEP due to electronegative regions. The interaction of ligand molecule with appropriate proteins has been obtained and hence neurotransmission activities in the brain have been explained.

Influence of calcium and magnesium on the secondary structure in solutions of individual caseins and binary casein mixtures

The influence of Ca and Mg addition on the secondary structure of αS1-, αS2-, β- and κ-CN in solutions of individual and binary mixtures of caseins was investigated using FTIR spectroscopy. Both in individual and their binary mixtures, addition of Ca and Mg resulted in increase in β-sheet structures and decrease in triple helices and turns, implying binding of cations to similar sites. Binding of cations with phosphoseryl clusters with loop-helix-loop motifs explained the reduction in helical element. In addition, the binding of cations to electronegative regions reduced electrostatic repulsion, resulting in an increase in hydrophobic interactions accounting for increase in sheet structures. Compared with Mg, it seemed that Ca had more affinity for caseins, especially when they were in a binary mixture. The information presented here expands the present understanding of casein interactions.

Investigation of bond topological and electrostatic properties of plumbagin molecule: An experimental and theoretical charge density study

Plumbagin is a naturally occurring derivative with several medicinal properties including antioxidants, antifungal, antimalarial, leprosy and antitumor properties; their structural and electrostatic properties are yet to be determined. The crystal structure of plumbagin has been solved; it shows that the compound crystallizes in P21/c space group with two molecules in the asymmetric unit. The electron density distribution of both molecules have determined from multipole model refinement. Among all the C–O bonds of both molecules (I & II), the OH group connected C–O bond and the methyl group connected C–C bond exhibits less electron density and the negative Laplacian of electron density as well. Further, the electrostatic potential (ESP) surface of two plumbagin molecules show some difference in their electronegative regions. The carbonyl O-atoms exhibit high electronegative ESP regions which are the key reactive locations of plumbagin when bind with the active site of target protein and in the ESP map, an aromatic π-cloud also observed in one of the molecule. The electron density distribution of O–H⋅⋅⋅O intermolecular interactions between the molecules I and II, reveals that these interactions are found very stronger than the other interactions in the crystal.

Charge density view on bicalutamide molecular interactions in the monoclinic polymorph and androgen receptor binding pocket

High-resolution single-crystal X-ray measurements of the monoclinic polymorph of bicalutamide and the aspherical atom databank approach have served as a basis for a reconstruction of the charge density distribution of the drug and its androgen receptor (AR) and albumin complexes. The contributions of various types of intermolecular interactions to the total crystal energy or ligand:AR energy were estimated. The cyan and amide groups secured the ligand placement in the albumin (Lys-137) and the AR binding pocket (Leu-704, Asn-705, Arg-752), and also determined the packing of the small-molecule crystals. The total electrostatic interaction energy on average was -230 kJ mol-1, comparable with the electrostatic lattice energy of the monoclinic bicalutamide polymorph. This is the result of similar distributions of electropositive and electronegative regions on the experimental and theoretical molecular electrostatic potential maps despite differences in molecular conformations. In general, bicalutamide interacted with the studied proteins with similar electrostatic interaction energies and adjusted its conformation and electrostatic potential to fit the binding pocket in such a way as to enhance the interactions, e.g. hydrogen bonds and π⋯π stacking.

Experimental and theoretical charge density, intermolecular interactions and electrostatic properties of metronidazole.

Metronidazole is a radiosensitizer; it crystallizes in the monoclinic system with space group P21/c. The crystal structure of metronidazole has been determined from high-resolution X-ray diffraction measurements at 90 K with a resolution of (sin θ/λ)max = 1.12 Å-1. To understand the charge-density distribution and the electrostatic properties of metronidazole, a multipole model refinement was carried out using the Hansen-Coppens multipole formalism. The topological analysis of the electron density of metronidazole was performed using Bader's quantum theory of atoms in molecules to determine the electron density and the Laplacian of the electron density at the bond critical point of the molecule. The experimental results have been compared with the corresponding periodic theoretical calculation performed at the B3LYP/6-31G** level using CRYSTAL09. The topological analysis reveals that the N-O and C-NO2 exhibit less electron density as well as negative Laplacian of electron density. The molecular packing of crystal is stabilized by weak and strong inter- and intramolecular hydrogen bonding and H...H interactions. The topological analysis of O-H...N, C-H...O and H...H intra- and intermolecular interactions was also carried out. The electrostatic potential of metronidazole, calculated from the experiment, predicts the possible electrophilic and nucleophilic sites of the molecule; notably, the hydroxyl and the nitro groups exhibit large electronegative regions. The results have been compared with the corresponding theoretical results.

Topological and electrostatic properties of diclofenac molecule as a non-steroidal anti-inflammatory drug: An experimental and theoretical study

Diclofenac is a Non-Steroidal Anti-Inflammatory Drug (NSAID), which highly inhibits the lipoxygenase pathways and reduces the formation of leukotriene lipids. In this work, we report on measurements and calculations of the electron density of Diclofenac, obtained from high resolution experimental X-ray diffraction data at 110 K and theoretical calculations. The supramolecular structure is dominated by the formation of a dimer through COOH homo-synthon. The analysis of the molecular electron density (by means of quantum theory of atoms in molecules), the electrostatic potential, the crystal packing and intermolecular interactions (through Hirshfeld surface analysis) enables gaining more insight into the nature of the molecule and its ability to interact with other molecules. Furthermore, the topological properties of the dimer interactions in both the crystal phase and human transthyretin protein environment were identified. The electrostatic potential map shows that the high electronegative regions appear around the carboxyl group of the diclofenac molecule in both the crystal and protein environment. This study is complemented by a molecular dynamics simulation of the interaction of diclofenac with transthyretin protein, which enables to test the hypothesis made with the charge density analysis.

Nitrofurantoin-melamine monohydrate (cocrystal hydrate): Probing the role of H-bonding on the structure and properties using quantum chemical calculations and vibrational spectroscopy

Cocrystal monohydrate of nitrofurantoin (NF) with melamine (MELA) has been studied as NF is an antibacterial drug used for the treatment of urinary tract infections. The structure of nitrofurantoin-melamine-monohydrate (NF-MELA-H2O) is characterized by FT-IR and FT-Raman spectroscopy. The energies and vibrational frequencies of the optimized structures calculated using quantum chemical calculations. Supported by normal coordinate analyses and potential energy distributions (PEDs), the complete vibrational assignments recommended for the observed fundamentals of cocrystal hydrate. With the aim of inclusion of all the H-bond interactions, dimer of NF-MELA-H2O has been studied as only two molecules of cocrystal hydrate are present in the unit cell. By the study of dimeric model consistent assignment of the FT-IR and FT-Raman spectrum obtained. H-bonds are of essential importance in an extensive range of molecular sciences. The vibrational analyses depict existence of H-bonding (O-H⋯N) between water O-H and pyridyl N atom of MELA in both monomer and dimer. To probe the strength and nature of H-bonding in monomer and dimer, topological parameters such as electron density (ρBCP), Laplacian of electron density (∇2ρBCP), total electron energy density (HBCP) and H-bond energy (EHB) at bond critical points (BCP) are evaluated by quantum theory of atoms in molecules (QTAIM). Natural bond orbitals (NBOs) analyses are carried out to study especially the intra and intermolecular H-bonding and their second order stabilization energy (E(2)). The value of HOMO-LUMO energy band gap for NF-MELA-H2O (monomer and dimer both) is less than NF, showing more chemical reactivity for NF-MELA-H2O. Chemical reactivity has been described with the assistance of electronic descriptors. Global electrophilicity index (ω = 7.3992 eV) shows that NF-MELA-H2O behaves as a strong electrophile than NF. The local reactivity descriptors analyses such as Fukui functions, local softnesses and electrophilicity indices performed to determine the reactive sites within NF-MELA-H2O. In MEP map of NF-MELA (monomer and dimer) electronegative regions are about NO2 and C=O group of NF, although the electropositive regions are around NH2, N-H group and H2O molecule. Molar refractivity (MR) value of NF-MELA-H2O (monomer and dimer) lies within the range set by Lipinski's modified rules. This study could set as an example to study the H-bond interactions in pharmaceutical cocrystals.

Investigation of the chemical and optical properties of halogen-substituted N-methyl-4-piperidone curcumin analogs by density functional theory calculations.

Halogen-substituted N-methyl-4-piperidone curcumin analog compounds were studied for their molecular structure, molecular vibration analysis, natural bond orbital, ultraviolet spectra, molecular reactivity analysis, and nonlinear optical properties. The molecules in interest were the (3E,5E)-3,5-dibenzylidene-1-methylpiperidin-4-one along with its substituted halogen (X = F- or Cl- or Br-) at the ortho, meta and para position in the phenyl ring. The calculated geometrical parameters at B3LYP/6-311++G(d,p) were in good agreement with the available experimental XRD data. Using the frequency calculations, the molecular vibrational modes have been analyzed. Meanwhile, the hyperconjugative stabilization energies have been calculated using NBO analysis to address the donor and acceptor in the hyperconjugation. The calculated UV spectra at TD-CAM-B3LYP/6-311++G(d,p) show strong absorption around 300 to 320 nm which corresponds to the absorption in the UV-A and UV-B region. From molecular electrostatic potential surface, CO moiety is one of the electronegative regions in the compounds where the CX moiety is the other electronegative region of the compounds. Fluoro-substituted compounds are the compounds with the most electronegativity while bromo-substituted compounds are the compounds with the least electronegativity. Calculations of average local ionization energy surfaces have been performed to obtain information related to the local reactivity of the molecules where the phenyl becomes less reactive after the substitution. The calculated first hyperpolarizability is 6 to 17 times larger than urea, the standard nonlinear optic material. These findings imply that all of the molecules considered have potential to be applied as active sunscreen material or nonlinear optic material.

Topology of electron density and electrostatic potential of HIV reverse transcriptase inhibitor zidovudine from high resolution X-ray diffraction and charge density analysis

Azidothymidine (AZT) is a first anti-HIV drug namely Zidovudine used for HIV treatment, which binds to the viral DNA primer and inhibits the HIV reverse transcription. The side effects of this powerful drug are severe and the detailed understanding of its electronic structure helps to design new drugs from the AZT molecule. Present study aims to determine the structure of AZT at electronic level from the experimental charge density analysis as well as the solid state DFT calculations. AZT was crystallized and low temperature high resolution X-ray diffraction intensity data has been measured up to sin (θ/λ)max = 1.1 Å−1 at 100.0 (2) K. The crystal structure of AZT was determined, which reveals the information that the AZT compound crystallizes with two molecules in the asymmetric unit which are conformationally different and linked through strong hydrogen bonding interactions (dimer). The Hirshfeld surface of both molecules shows the locations of weak and strong interactions. Further, a multipole model refinement was carried out using Hansen-Coppens multipole formalism. The experimental topological properties of electron density of AZT molecules were determined and compared with the results of theoretical DFT calculations based on solid state and gas phase studies. The charge density distribution of the two molecules in the asymmetric unit is unequal and shows some difference. The topological properties of O–H⋅⋅⋅O, O–H⋅⋅⋅N, C–H⋅⋅⋅N, H⋅⋅⋅H and azide⋅⋅⋅azide group interactions are also determined. The electrostatic potential (ESP) surface of both AZT molecules in the crystal exhibits high electronegative regions around the O, N atoms and also around the azide group, however, ESP regions of molecules (I) and (II) are not similar.

Synthesis, crystal structure and Hirshfeld surface of 2-Amino-3 benzyloxy pyridinium picrate (1:1)

Abstract The crystal and molecular structure of 2-amino-3-benzyloxy pyridinium picrate (ABPP) have been elucidated using spectroscopic (MS, NMR and FTIR) and single crystal X-ray diffraction. In ABPP, the piperidene and phenyl ring are perpendicular to each other and intramolecular hydrogen bonds (N2⋯H2B⋯O1 and C12⋯H12⋯O1) are observed. The intermolecular hydrogen bonds of the type C6⋯H6B⋯O2, C3⋯H3⋯O5 and N2⋯H2C⋯O7 connects the molecules within the crystal structure. Intermolecular interactions are visualized and quantified using Hirshfeld surfaces computational method. The intercontact, O⋯H contributes more to the Hirshfeld surfaces in both molecules. The electrostatic potential surfaces plotted over the co-crystal signify the electropositive and electronegative regions over the co-crystals. The thermo gravimetric analysis (TGA) measurement provided the thermal degradation of the ABPP to be from 230–320 °C. In addition, the emission spectrum was measured using fluorescence spectrometer and the ABPP was excited at 321 nm.

Crystal structure and theoretical charge density studies of dilantin molecule

Dilantin molecule is an inhibitor of multiple protein targets such as prostate-specific antigen, lung cancer cells and it also reduces the tumor growth and invasion of the breast metastatic cancer cells. Understanding the precise geometry, charge density distribution and electrostatic properties of inhibitor pertain to predict the active site interaction between the inhibitor and receptor. Hence, the present study is aimed to determine these parameters through experimental and theoretical studies. Dilantin molecule crystallizes in orthorhombic system with Pna21 space group. The crystal and the molecular structure of dilantin molecule has been redetermined using X-ray crystal structure analysis. The two phenyl rings and imidazolidine ring in the molecule are not in coplanar and oriented in different directions, the dihedral angles are 66.6(3) and 65.3(3)°. The molecular packing of crystal is stabilized by strong NH⋯O and weak CH⋯O intermolecular hydrogen bonding interactions. A theoretical charge density analysis has been performed for the molecule lifted from the crystal, reveals the charge density distribution of dilantin molecule, this result has been compared with the corresponding gas phase studies. The electrostatic properties of the molecule also calculated. The calculated dipole moment of dilantin molecule in the crystal phase is (2.88 D), which is not very much different from its gas phase value (2.68 D). The electrostatic potential map displays strong electronegative regions near the O and N atoms, which are the possible reactive locations of the molecule.

Nanoscale Patterns on Polar Oxide Surfaces

Polar ionic surfaces with bulk termination are inherently unstable because of their diverging electrostatic surface energy. Nevertheless, they are frequently observed in nature, mainly because of charge neutralization by adsorbates, but occur also under atomically clean conditions. Several mechanisms have been invoked to explain the stability of atomically clean polar surfaces, but the frequently observed periodic nanoscale pattern formation has not yet been explained. Here we propose that long-range interactions between alternating electropositive and electronegative regions of different surface terminations minimize the electrostatic energy of the surface and thus stabilize the nanoscale pattern. This is illustrated using the example of polar Fe oxide surfaces by combining scanning tunneling microscopy and spectroscopy results with results from density functional theory-based calculations and dipole–dipole interaction models.

Spectroscopic characterization of 4-[2-(5-Ethylpyridin-2-yl)ethoxy]benzaldehyde oxime and investigation of its reactive properties by DFT calculations and molecular dynamics simulations

The molecular structure, vibrational wave numbers, NLO, NBO, MEP and HOMO, LUMO analysis of 4-[2-(5-Ethylpyridin-2-yl)ethoxy]benzaldehyde oxime were reported. The theoretically predicted geometrical parameters are in agreement with the XRD data. Using NBO analysis the change in the electron density in the anti-bonding orbital and stabilization energies have been calculated to give clear evidence of stabilization in the hyper-conjugation of hydrogen bonded interactions. The calculated first hyperpolarizability is 46.761 times that of the standard NLO material urea. From molecular electrostatic potential plot, phenyl ring, pyridine ring and oxygen atoms are the most electronegative regions and the hydrogen atom in the OH group is the most electropositive region. ALIE surfaces and Fukui functions have been calculated in order to obtain information related to the local reactivity properties of the title molecule. Intra-molecular non-covalent interactions have also been searched for. In order to investigate autoxidation and degradation properties we have calculated bond dissociation energies for all single acyclic bonds. To determine which atoms have the most pronounced interactions with water molecules we have conducted molecular dynamics simulations and calculated radial distribution functions. Molecular docking studies suggest that the title compound can be a lead compound for developing new anti-cancerous drug.

Probing the effect of nitro groups in nitramine based energetic molecules: a DFT and charge density study

The structure, electron density distribution, energetic and electrostatic properties of simple nitramine based energetic TMA, DMNA, MDA and TNA molecules were determined using density functional theory (B3LYP) with the 6-311G** and aug-cc-pVDZ basis sets coupled with Bader's theory of atoms in molecules. In the NO2 group substituted molecules, the N–N bond distance increases with the increase of NO2 groups, whereas in C–N bonds, this effect is relatively less, and the distances are almost equal. The topological analysis of electron density reveals that the electron density ρbcp(r) of C–N and N–N bonds are significantly decreasing with the increase of NO2 groups in the nitramine molecules. The Laplacian of electron density ▽2ρbcp(r) of N–NO2 bonds [DMNA: − 16.7 eÅ− 5, MDA: − 12.8 eÅ− 5 and TNA: − 7.9 eÅ− 5] of the molecules are relatively less negative, and the values also decrease with the increase of NO2 groups; this implies that the charge concentration decreases with the increase of NO2 groups, which leads to weakening the N–N bonds of the molecules. The isosurface of molecular electrostatic potential displays high electronegative regions around the NO2 groups. The oxygen balance OB100 of the molecules increases as the number of NO2 group increases in the molecules, in which, the TNA molecule having maximum OB100 value [+7.89]. The band gap, heat of detonation, bond dissociation energy and charge imbalance are predominantly depends on the number of NO2 group present in the molecule. The charge imbalance parameter (ν) has been calculated for all molecules, which reveals that TNA is a highly sensitive molecule, the corresponding ν value is 0.047.

Intermolecular interactions, charge-density distribution and the electrostatic properties of pyrazinamide anti-TB drug molecule: an experimental and theoretical charge-density study.

An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data [(sin θ/λ)max = 1.1 Å(-1)] measured at 100 (2) K. The structure was solved by direct methods using SHELXS97 and refined by SHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen-Coppens multipole formalism implemented in the XD software. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained from CRYSTAL09 at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N-H...N and N-H...O hydrogen bonds, in which the N3-H3B...N1 and N3-H3A...O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N...H and O...H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the π-electron cloud.