HOMO-LUMO Plot Research Articles

Probing vibrational activities, electronic properties, molecular docking and Hirshfeld surfaces analysis of 4-chlorophenyl ({[(1E)-3-(1H-imidazol-1-yl)-1-phenylpropylidene]amino}oxy)methanone: A promising anti-Candida agent

The promising anti-Candida agent, 4-chlorophenyl ({[1E-3(1H-imidazole-1-yl)-1-phenylpropylidene}oxy)methanone (4-CPIPM) was comprehensively characterized by FT-IR, FT-Raman, UV, as well as 1H and 13C spectroscopic techniques. The theoretical calculations in the current study utilized Gaussian 09 W software with DFT approach of the B3LYP/6-311++G(d,p) method. The experimental X-ray diffraction data of the 4-CPIPM molecule were compared with the optimized structure and showed well agreement. Intermolecular electronic interactions and their stabilization energies have been analyzed by natural bond orbital method. Potential energy distribution confirmed the normal fundamental mode of vibration with the aid of MOLVIB software. The chemical shift values of the 1H and 13C spectra of the title compound were computed using gauge independent atomic orbital and the results were compared with the experimental values. The time-dependent density function theory method was used to predict the electronic, absorption wavelength and frontier molecular orbital energies. The HOMO-LUMO plots proved the charge transfer in the molecular system of the title compound through conjugated paths. The molecular electrostatic potential analysis provided the electrophilic and nucleophilic reactive sites in the title molecule which have been analyzed using Hirshfeld surface and two dimensions fingerprint plots. Non covalent interactions were also studied using reduced density gradient analysis and color filled electron density diagram. Molecular docking studies of the ligand-protein interactions along with their binding energies were carried out aiming to explain the potent anti-Candida activity of the title molecule.

Design and Electronic Characterization of Bio-Molecular QCA: A First Principle Approach

Molecular Quantum-dot Cellular Automata is the most promising and challenging technology nowadays for its high operating frequency, extremely high device density and non-cryogenic working temperature. In this paper, we report a First Principle approach based on analytical model of 3-dot Bio Molecular Quantum-dot Cellular Automata. The device is 19.62Å long and this bio molecular Quantum dot Cell has been made with two Adenine Nucleotide bio-molecules along with one Carbazole and one Thiol group. This whole molecular structure is supported onto Gold substrate. In this paper, two Adenine Nucleotides act as two quantum dots and Carbazole acts as another dot. These 3-Quantum-dots are mounted in a tree like structure supported with Thiol group. This model has been demonstrated with Extended Hückel Theory based semi-empirical method. The quantum ballistic transmission and HOMO-LUMO plot support the polarization state change. This state changing ability has been observed for this molecular device. Therefore, this property has been investigated and reported in this paper. HOMO-LUMO plot shows the two logic states along with null state for this 3-dots system. This phenomenon illustrates how the charge transfers take place. Two polarization states along with one additional null state have been obtained for this bio molecular nano device. This molecular device has been operated with 1000THz frequency. This nanoscale design approach will initiate one step towards the modeling of high frequency bio molecular Quantum dot Cell at room temperature.

Structural, spectral, quantum chemical and thermal studies on a new NLO crystal: guanidinium cinnamate

New organic non-linear optical (NLO) single crystals of guanidinium cinnamate were crystallized by solvent evaporation solution growth technique and the crystal and molecular structure were determined by single crystal X-ray diffraction. The crystal packing is dominated by classical N–H···O hydrogen bonding interactions. Due to deficiency of acceptor atoms compared to the donor sites, two unusual ring R2 1(6) motifs are formed through two N–H···O hydrogen bonds. These ring motifs are further connected through chain C2 2(6) or C2 2(8) motifs along the b-axis of the unit cell. Further, these chain and ring motifs are cross-linked through another N–H···O hydrogen bond leading to classical ring R2 2(8) motif. These chain and ring motifs are interlinked with each other to form secondary ring R6 6(14)/R6 6(16) motifs. The molecular geometry of the asymmetric part of the unit cell was optimized theoretically by density functional theory using the B3LYP function with 6-311 + + G(d,p) basis set. The optimized molecular geometry and computed vibrational spectra are compared with experimental results which showed significant agreement. The intermolecular interactions of the title compound were analyzed by the Hirshfeld surfaces. The computed hyperpolarizability values showed that the compound is a good candidate for NLO applications. The chemical hardness, electro-negativity and chemical potential of the molecule were computed by HOMO–LUMO plot. The lower band gap of the frontier orbitals indicates the suitability of fabrication of the material for non-linear optoelectronic applications.

Synthesis, vibrational spectroscopic investigations, molecular docking, antibacterial studies and molecular dynamics study of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole

Antimicrobial active 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole (NATPB) was synthesized and observed IR, Raman bands are compared with the theoretically predicted wave numbers. In the IR spectrum the NH stretching wave number splits into a doublet with a noted difference and is red shifted from the computed value, which indicates the weakening of NH bond resulting in proton transfer to the neighbouring oxygen atom. The HOMO-LUMO plots reveal the charge transfer in the molecular system through the conjugated paths. The electrophilic and nucleophilic reactive sites are identified from the MEP plot. Mapping of average local ionization energy (ALIE) values to the electron density surface served us as a tool for prediction of molecule sites possibly prone to electrophilic attacks. Other important reactive centres of the title molecule were detected by calculations of Fukui functions. Calculations of bond dissociation energies (BDE) for hydrogen abstraction were used in order to assess whether the NATPB molecules is prone to autoxidation mechanism or not, while BDE of the remaining single acyclic bonds were used in order to determine the weakest bond. Interaction properties with water were investigated by molecular dynamics (MD) simulations and calculations of radial distribution functions (RDFs). The compound possessed broad spectrum activity against all of the tested Gram-positive and Gram-negative bacteria and yeasts, their minimum inhibitory concentrations (MICs) ranging between 32 and 128 μg/ml. The compound exhibited significant antibacterial activity (32 μg/ml) against an antibiotic resistant E. faecalis isolate, at same potency with the compared standard drugs vancomycin and gentamycin sulfate. The molecular docking studies show that the compound might exhibit inhibitory activity against CDK inhibitors.

Spectroscopic characterization of 1-[3-(1H-imidazol-1-yl)propyl]-3-phenylthiourea and assessment of reactive and optoelectronic properties employing DFT calculations and molecular dynamics simulations

IR and Raman spectra of 1-[3-(1H-imidazol-1-yl)propyl]-3-phenylthiourea (HIPPT) have been recorded in the solid phase and the vibrational wave numbers are calculated theoretically by B3LYP/6-31G(d,p) (6D, 7F) method. All the fundamental vibrational modes have been assigned using potential energy distribution values and the molecular structure was analyzed in terms of parameters like bond length, bond angles and dihedral angles. The ring breathing mode of the phenyl ring is observed at 1016 cm−1 in the IR spectrum, 1014 cm−1 in the Raman spectrum and at 1014 cm−1 theoretically. The values of polarizability and hyperpolarizabilities were calculated and nonlinear optical properties are discussed. The HOMO-LUMO plot reveals the charge transfer possibilities in the molecule. The NBO analysis was computed and possible transitions were correlated with the electronic transitions. In the title compound, the imidazole ring and CH2 groups are tilted from each other and the thiourea group is tilted from the phenyl ring. Using MEP plot the electrophilic and nucleophilic regions are identified. Local reactivity properties were investigated by analysis of ALIE surfaces and Fukui functions. Oxidation and degradation properties were initially assessed by calculation of bond dissociation energies of all single acyclic bonds. Determination of atoms with pronounced interactions with water molecules was performed by calculation of radial distribution functions after molecular dynamics simulations. Chargehopping rates were calculated within Marcus semi-empiric approach, employing both DFT calculations and MD simulations. The molecular docking computational predictions were complemented by the in vitro antibacterial activity evaluation.

Structural and vibrational spectral studies on hydrogen bonded salts: 4-chloroanilinium maleate and nitrate

In the present study, proton transfer from nitric and maleic acids to amine group (4-chloroaniline) led to hydrogen bonded crystals of 4-chloroanilinium maleate (4CAM) and 4-chloroanilinium nitrate (4CAN) which are investigated by the experimental and theoretical approaches. The molecular structures of these two compounds were optimized with the Density Functional Theory (DFT) using B3LYP function and the Hartree-Fock (HF) level with a6-311 ++G(d,p) basis set. Geometrical parameters of the molecules were also analyzed along with their intermolecular hydrogen bond, which tailors the ions. These analyses show that present molecules are stabilized through the N–H ⋯O and O–H ⋯O hydrogen bonds. The vibrational modes were computed by quantum chemical methods. Further, these modes are investigated by FT-IR and FT-Raman spectroscopy in the range of 4000–400 cm−1. The optimized molecular geometry and computed vibrational spectra are compared with experimental results, which show significant agreement. The natural bond orbital (NBO) analysis was carried out to interpret hyperconjucative interaction and intramolecular charge transfer (ICT). This analysis gives the precise insight into the nature of H-bond interactions. The chemical hardness, electronegativity and chemical potential of the molecules were determined by HOMO–LUMO plot. The frontier molecular orbitals have small band gap value, which signify the possible biological/pharmaceutical activity of the compounds. The proton transfer from the nitric and maleic acids to amine group (of 4-chloroaniline) lead to hydrogen bonded crystals of 4-chloroanilinium maleate (4CAM) and 4-chloroanilinium nitrate (4CAN). The molecular structures of these two compounds were optimized with the Density Functional Theory (DFT) and Hartree-Fock (HF) methods. Geometrical parameters of the molecules were analyzed along with their intermolecular hydrogen bond which tailors the ions. These analyses show that the molecular aggregations are stabilized through the N–H···O and O– H···O hydrogen bonds. The vibrational modes were computed by quantum chemical methods and further investigated by FT-IR and FT- Raman spectroscopy in the range of 4000–400 cm-1.

Single crystal XRD, vibrational spectra, quantum chemical and thermal studies on a new semi-organic crystal: 4-Aminium antipyrine chloride

The new semi-organic crystal of 4-aminium antipyrine chloride was grown as a single crystal by slow evaporation solution growth method. The crystal and molecular structure of the grown crystal was determined by single crystal diffraction techniques. The single crystal XRD studies reveal that the phenyl ring and pyrazolone ring of the cation has been inclined at an angle of 52.3 (1)°. The molecular aggregations were stabilized through intricate three dimensional hydrogen bonding network formed by the classical N–H⋯O and N–H⋯Cl hydrogen bonds. The cationic dimer R22(10) motif formed through N–H⋯O intermolecular hydrogen bonds was observed around the inversion center of the unit cell. The amino group from the cation and the chlorine anion was linked through N–H⋯Cl intermolecular hydrogen bond leading to a R24 (8) ring motif. These two ring motifs were extended along the a-axis of the unit cell and forms a hydrophilic layer at z = 0 and 1, which is sandwiched between the hydrophobic layer at z = 1/2. Geometry optimization of the molecules was done by Density Functional Theory (DFT) using the B3LYP function and Hartree–Fock (HF) level with 6-311++G(d,p) basis set. The optimized molecular geometry and computed vibrational spectra were compared with experimental results which show a significant agreement. The natural bond orbital (NBO) analysis was carried out to interpret hyperconjucative interaction and intramolecular charge transfer (ICT). The chemical hardness, electro-negativity and chemical potential of the molecule were carried out by HOMO-LUMO plot. The lower band gap value of the frontier orbitals shows the possible bioactivity of the molecule.

Hydrogen bonding motifs, spectral characterization, theoretical computations and anticancer studies on chloride salt of 6-mercaptopurine: An assembly of corrugated lamina shows enhanced solubility

6-Mercaptopurine (an anti cancer drug), is coming under the class II Biopharmaceutics Classification System (BCS). In order to enhance the solubility with retained physiochemical/pharmaceutical properties, the present work was attempted with its salt form. The single crystals of 6-mercaptopurinium chloride (6MPCl) were successfully grown by slow evaporation technique under ambient temperature. The X-ray diffraction study shows that the crystal packing is dominated by N–H⋯Cl classical hydrogen bonds leading to corrugated laminar network. The hydrogen bonds present in the lamina can be dismantled as three chain C21(6), C21(7) and C21(8) motifs running along ab-diagonal of the unit cell. These primary chain motifs are interlinked to each other forming ring R63(21) motifs. These chain and ring motifs are aggregated like a dendrimer structure leading to the above said corrugated lamina. This low dimensional molecular architecture differs from the ladder like arrays in pure drug though it possess lattice water molecule in lieu of the chloride anion in the present compound. Geometrical optimizations of 6MPCl were done by Density Functional Theory (DFT) using B3LYP function with two different basis sets. The optimized molecular geometries and computed vibrational spectra are compared with their experimental counterparts. The Natural Bond Orbital (NBO) analysis was carried out to interpret hyperconjugative interaction and Intramolecular Charge Transfer (ICT). The chemical hardness, electronegativity, chemical potential and electrophilicity index of 6MPCl were found along with the HOMO–LUMO plot. The lower band gap value obtained from the Frontier Molecular Orbital (FMO) analysis reiterates the pharmaceutical activity of the compound. The anticancer studies show that 6MPCl retains its activity against human cervical cancer cell line (HeLa). Hence, this anticancer efficacy and improved solubility demands 6MPCl towards the further pharmaceutical applications.

Single crystal XRD, vibrational and quantum chemical calculation of pharmaceutical drug paracetamol: A new synthesis form

The common house hold pharmaceutical drug, paracetamol (PAR), has been synthesized from 4-chloroaniline as a first ever report. After the synthesis, good quality single crystals were obtained for slow evaporation technique under the room temperature. The crystal and molecular structures were re-determined by the single crystal X-ray diffraction. The vibrational spectral measurements were carried out using FT-IR and FT-Raman spectroscopy in the range of 4000–400cm−1. The single crystal X-ray studies shows that the drug crystallized in the monoclinic system polymorph (Form-I). The crystal packing is dominated by NH⋯O and OH⋯O classical hydrogen bonds. The ac diagonal of the unit cell features two chain C(7) and C(9) motifs running in the opposite directions. These two chain motifs are cross-linked to each other to form a ring R44(22) motif and a chain C22(6) motif which is running along the a-axis of the unit cell. Along with the classical hydrogen bonds, the methyl group forms a weak CH⋯O interactions in the crystal packing. It offers the support for molecular assembly especially in the hydrophilic regions. Further, the strength of the hydrogen bonds are studied the shifting of vibrational bands. Geometrical optimizations of the drug molecule were done by the Density Functional Theory (DFT) using the B3LYP function and Hartree–Fock (HF) level with 6-311++G(d,p) basis set. The optimized molecular geometry and computed vibrational spectra are compared with experimental results which show significant agreement. The factor group analysis of the molecule was carried out by the various molecular symmetry, site and factor group species using the standard correlation method. The Natural Bond Orbital (NBO) analysis was carried out to interpret hyperconjugative interaction and intramolecular charge transfer (ICT). The chemical softness, chemical hardness, electro-negativity, chemical potential and electrophilicity index of the molecule were found out first time by HOMO–LUMO plot. The frontier orbitals shows lower band gap values signify the possible biological/pharmaceutical activity of the molecule. The thermodynamical properties are also obtained from the calculated frequencies of the optimized structures.

XRD, vibrational spectra and quantum chemical studies of an anticancer drug: 6-Mercaptopurine

The single crystal of the hydrated anticancer drug, 6-Mercaptopurine (6-MP), has been grown by slow evaporation technique under room temperature. The structure was determined by single crystal X-ray diffraction. The vibrational spectral analysis was carried out using Laser Raman and FT-IR spectroscopy in the range of 3300–100 and 4000–400cm−1. The single crystal X-ray studies shows that the crystal packing is dominated by N–H⋯O and O–H⋯N classical hydrogen bonds leading to a hydrogen bonded ensemble. This classical hydrogen bonds were further connected through O–H⋯S hydrogen bond to form two primary ring R44(16) and R44(12) motifs. These two primary ring motifs are interlinked with each other to build a ladder like structure. These ladders are connected through N–H⋯N hydrogen bond along c-axis of the unit cell through chain C(5) motifs. Further, the strength of the hydrogen bonds is studied through vibrational spectral measurements. The shifting of bands due to the intermolecular interactions was also analyzed in the solid crystalline state. Geometrical optimizations of the drug molecule were done by Density Functional Theory (DFT) using the B3LYP function and Hartree–Fock (HF) level with 6-311++G(d,p) basis set. The optimized molecular geometry and computed vibrational spectra are compared with experimental results which show significant agreement. The natural bond orbital (NBO) analysis was carried out to interpret hyperconjugative interaction and intramolecular charge transfer (ICT). The chemical hardness, electro-negativity and chemical potential of the molecule are carried out by HOMO–LUMO plot. In which, the frontier orbitals has lower band gap value indicating the possible pharmaceutical activity of the molecule.

Molecular structure, vibrational spectral investigation and the confirmation analysis of 4-Methylesculetin molecule

In this work, FT-IR, FT-Raman, and FT-NMR spectra of 4-Methylesculetin molecule are presented for the first time. FT-IR, FT-Raman, and FT-NMR spectra of 4MEC have been recorded and analyzed. The FT-IR and FT-Raman spectra of this molecule are recorded at 4000-400 cm−1 and 50–3500 cm−1, respectively. The infrared vibrational frequencies, absolute intensities, potential energy profile, HOMO-LUMO plot and NBO analysis of the molecule have been also predicted using Becke’s three-parameter hybrid B3LYP method in the density functional theory DFT method. Calculated and experimental data are in good agreement.