Molecular structure, anharmonic vibrational frequencies and NBO analysis of naphthalene acetic acid by density functional theory calculations

Investigating the potential of monocyclic B9N9 and C18 rings for the electrochemical sensing, and adsorption of carbazole-based anti-cancer drug derivatives: DFT-based first-principle study

CONTEXT

For the first time, the use of monocyclic rings C18 and B9N9 as sensors for the sensing of carbazole-based anti-cancer drugs, such as tetrahydrocarbazole (THC), mukonal (MKN), murrayanine (MRY), and ellipticine (EPT), is described using DFT simulations and computational characterization. The geometries, electronic properties, stability studies, sensitivity, and adsorption capabilities of C18 and B9N9 counterparts towards the selected compounds confirm that the analytes interact through active cavities of the C18 and B9N9 rings of the complexes.

METHODS

Based on the interaction energies, the sensitivity of surfaces towards EPT, MKN, MRY, and THC analytes is observed. The interaction energy of EPT@B9N9, MKN@B9N9, MRY@B9N9, and THC@B9N9 complexes are observed - 20.40, - 19.49, - 20.07, and - 18.27 kcal/mol respectively which is more exothermic than EPT@C18, MKN@C18, MRY@C18, and THC@C18 complexes are - 16.37, - 13.97, - 13.96, and - 11.39 kcal/mol respectively. According to findings from the quantum theory of atoms in molecules (QTAIM) and the reduced density gradient (RDG), dispersion forces play a significant role in maintaining the stability of these complexes. The electronic properties including FMOs, density of states (DOS), natural bond orbitals (NBO), charge transfer, and absorption studies are carried out. In comparison of B9N9 and C18, the analyte recovery time for C18 is much shorter (9.91 × 10-11 for THC@C18) than that for B9N9 shorter recovery time value of 3.75 × 10-9 for EPT@B9N9. These results suggest that our reported sensors B9N9 and C18 make it faster to detect adsorbed molecules at room temperature. The sensor response is more prominent in B9N9 due to its fine energy gap and high adsorption energy. Consequently, it is possible to think of these monocyclic systems as a potential material for sensor applications.

Alkali metals doped cycloparaphenylene nanohoops: Promising nonlinear optical materials with enhanced performance

In the ongoing pursuit of novel and efficient NLO materials, the potential of alkali metal-doped {6}cycloparaphenylene ({6}CPP) and methylene bridged {6} cycloparaphenylene (MB{6}CPP) nanohoops as excellent NLO candidates has been explored. The geometric, electronic, linear, and nonlinear optical properties of designed systems have been investigated theoretically. All the nanohoops demonstrated thermodynamic stability, with remarkable interaction energies reaching up to -1.39 eV (-0.0511 au). Notably, the introduction of alkali metals led to a significant reduction in the HOMO-LUMO energy gaps, with values as low as 2.92 eV, compared to 6.80 eV and 6.06 eV for undoped {6}CPP and MB{6}CPP, respectively. Moreover, the alkali metal-doped nanohoops exhibited exceptional NLO response, with the K@r6-{6}CPP complex achieving the highest first hyperpolarizability of 56,221.7 × 10-30 esu. Additionally, the frequency-dependent first hyperpolarizability values are also computed at two commonly used wavelengths of 1550 nm and 1907 nm, respectively. These findings highlight the potential of designed nanohoops as promising candidates for advanced NLO materials with high-tech applications.

Density functional modeling, and molecular docking with SARS-CoV-2 spike protein (Wuhan) and omicron S protein (variant) studies of new heterocyclic compounds including a pyrazoline nucleus

Nowadays, different vaccines and antiviral drugs have been developed and their effectiveness has been proven against SARS-CoV-2. Pyrazoline derivatives are biologically active molecules and exhibit broad-spectrum biological activity properties. In this scope, four new molecules (4a-d) including a pyrazoline core were synthesized in order to predict their antiviral properties theoretically. Compounds 4a-d were purified by the crystallization method. The structures of 4a-d were completely characterized by NMR, IR, and elemental analysis. The molecular structures of the compounds in the ground state have been optimized using density functional theory with the B3LYP/6-31++G(d,p) level. The quantum chemical parameters were predicted by density functional theory calculations. Moreover, the molecular docking studies of 4a-d with SARS-CoV-2 Spike protein (Wuhan) and omicron S protein (variant) were presented to investigate and predict potential interactions. The binding sites, binding types and energies, bond distances of the non-covalent interactions and calculated inhibition constants (calc. Ki) as a consequence of molecular docking for 4a-d were presented in this study. Furthermore, the stability of the protein-4a complex obtained from the docking was investigated through molecular dynamics simulation.Communicated by Ramaswamy H. Sarma.

Deciphering the Role of Alkali Metals (Li, Na, K) Doping for Triggering Nonlinear Optical (NLO) Properties of T-Graphene Quantum Dots: Toward the Development of Giant NLO Response Materials

Nanoscale nonlinear optical (NLO) materials have received huge attention of the scientists in current decades because of their enormous applications in optics, electronics, and telecommunication. Different studies have been conducted to tune the nonlinear optical response of the nanomaterials. However, the role of alkali metal (Li, Na, K) doping on triggering the nonlinear optical response of nanomaterials by converting their centrosymmetric configuration into noncentrosymmetric configuration is rarely studied. Therefore, to find a novel of way of making NLO materials, we have employed density functional theory (DFT) calculations, which helped us to explore the effect of alkali metal (Li, Na, K) doping on the nonlinear optical response of tetragonal graphene quantum dots (TGQDs). Ten new complexes of alkali metal doped TGQDs are designed theoretically. The binding energy calculations revealed the stability of alkali metal doped TGQDs. The NLO responses of newly designed complexes are evaluated by their polarizability, first hyperpolarizability (β_o), and frequency dependent hyperpolarizabilities. The Li@r8a exhibited the highest first hyperpolarizability (β_o) value of 5.19 × 10⁵ au. All these complexes exhibited complete transparency in the UV region. The exceptionally high values of β_o of M@TGQDs are accredited to the generation of diffuse excess electrons, as indicated by NBO analysis and PDOS. NCI analysis is accomplished to examine the nature of bonding interactions among alkali metal atoms and TGQDs. Our results suggest alkali metal doped TGQD complexes as potential candidates for nanoscale NLO materials with sufficient stability and enhanced NLO response. This study will open new doors for making giant NLO response materials for modern hi-tech applications.

Structural, Electronic and NLO Properties of 6-aminoquinoline: A DFT/TD-DFT Study

A computational study based on the DFT/TD-DFT approach was performed to explore various properties of 6-aminoquinoline (6AQ). The geometrical parameters, molecular orbitals (MOs), electronic spectra, electrostatic potential, molecular surface, reactivity parameters and thermodynamic properties of 6AQ were explored. The absorption and emission spectra of 6AQ in solvents have been estimated by TD-DFT coupled with the PCM model and correlated with the available experimental results. Depending on the solvents, the computed absorption maxima of 6AQ were noticed between 327 nm - 340 nm and ascribed to [Formula: see text] transition. The simulated emission maxima were obtained between 389 to 407 nm and ascribed to [Formula: see text] transition. On increasing the solvent polarity, both the emission and absorption maxima showed a bathochromic shift. The LUMO and HOMO were localized on the entire molecule. It was observed that the lowest excited state is possibly the [Formula: see text] charge-transfer (CT) state. The natural bonding orbital (NBO) study points out that ICT plays a significant role in stabilizing the molecular system. Moreover, the NLO (nonlinear optical) properties (polarizability, first-order hyperpolarizability and dipole moment) were computed using different hybrid functionals. The estimated values indicate that 6AQ can be considered a desirable molecule for further studies of the NLO applications.

A study of plant growth regulators detection based on terahertz time-domain spectroscopy and density functional theory

Terahertz technology is receiving increasing attention for its use as an efficient non-destructive, non-contact and label-free optical method for qualitative and quantitative detection. The aim of this study was to develop a chemical analysis methodology based on terahertz time-domain spectra that could be used to detect plant growth regulators, such as glyphosine, naphthaleneacetic acid, daminozide and gibberellic acid. The THz fingerprint spectra of these four PGRs were located in the 0.3–1.8 THz, with the peaks of glyphosine at 0.32, 0.49, 0.74, 0.87, 0.96, and 1.49 THz; daminozide at 0.33, 0.39, 0.55, 0.67, and 1.17 THz; gibberellic acid at 0.46, 0.58, 0.92, and 1.38 THz and naphthaleneacetic acid at 0.43, 0.57, 0.73, and 0.90 THz. The results showed that these four plant growth regulators exhibited numerous distinct spectral features in frequency-dependent absorption spectra, which demonstrated the qualitative capacity of terahertz time-domain. The origin of the observed terahertz absorption peaks of these four plant growth regulators was determined through density functional theory calculations and analysis of absorption spectra. Discriminant analysis method was used to evaluate the classification trends of the four plant growth regulators based on their THz absorbance spectra. Generally, this study provides a reference for the rapid detection of plant growth regulators in fruits and vegetables by using terahertz spectroscopy technology.

Terahertz technology is receiving increasing attention for its use as an efficient non-destructive, non-contact and label-free optical method for qualitative and quantitative detection.

Electrochemically Active In Situ Crystalline Lithium-Organic Thin Films by ALD/MLD

Intercalated metal-organic framework (iMOF) type electrochemically active aromatic metal carboxylates are intriguing material candidates for various energy storage devices and microelectronics. In this work, we grow in situ crystalline thin films of such materials through atomic/molecular layer deposition (ALD/MLD); the remarkable benefit of this approach is the possibility to evaluate their electrochemical properties in a simple cell configuration without any additives. Five organic linkers are investigated in combination with lithium: terephthalic acid (TPA), 3,5-pyridinedicarboxylic acid (PDC), 2,6-naphthalenedicarboxylic acid (NDC), 4,4'-biphenyldicarboxylic acid (BPDC), and 4,4'-azobenzenedicarboxylic acid (AZO). In particular, the electrochemical activity of Li-PDC and the crystal structure of Li-AZO are addressed here for the first time. We believe that the in situ gas-phase thin-film deposition is a crucial requirement to benefit from the iMOF-type electrode materials in, e.g., microelectronics and wearable devices.

Theoretical insights into the competitive metal bioaffinity of lactoferrin as a metal ion carrier: a DFT study

Metal–protein complexes, specifically lactoferrin (Lf), an iron-binding glycoprotein found naturally in milk and several other body fluids play a pivotal role in all living organisms.

Synthesis, characterization, in-vitro antimicrobial properties, molecular docking and DFT studies of 3-{(E)-[(4,6-dimethylpyrimidin-2-yl)imino]methyl} naphthalen-2-ol and Heteroleptic Mn(II), Co(II), Ni(II) and Zn(II) complexes

Heteroleptic divalent metal complexes [M(L) (bipy)(Y)]•nH2O (where M = Mn, Co, Ni, and Zn; L = Schiff base; bipy = 2,2’-bipyridine; Y = OAc and n = 0, 1) have been synthesized from pyrimidine Schiff base ligand 3-{(E)-[(4,6-dimethylpyrimidin-2-yl)imino]methyl} naphthalen-2-ol, 2,2’-bipyridine and metal(II) acetate salts. The Schiff base and its complexes were characterized by analytical (CHN elemental analyses, solubility, melting point, conductivity) measurements, spectral (IR, UV-vis, 1H and 13C-NMR and MS) and magnetometry. The elemental analyses, Uv-vis spectra and room temperature magnetic moment data provide evidence of six coordinated octahedral geometry for the complexes. The metal complexes’ low molar conductivity values in dimethylsulphoxide suggested that they were non-ionic in nature. The compounds displayed moderate to good antimicrobial and antifungal activities against S. aureus, P. aeruginosa, E. coli, B. cereus, P. mirabilis, K. oxytoca, A. niger, A. flevus and R. Stolonifer. The compounds also exhibited good antioxidant potentials with ferrous ion chelation and, 1-diphenyl-2-picryl-hydrazyl (DPPH) radical scavenging assays. Molecular docking studies showed a good interaction with drug targets used. The structural and electronic properties of complexes were further confirmed by density functional theory calculations.

Anharmonic vibrational spectral analysis of L-(-)-xylose molecule

In this work, a detailed vibrational analysis of L-(-)-xylose molecule has been carried out. The geometrical parameters and anharmonic spectrum have been calculated and compared with XRD, FTIR (4000–400[Formula: see text]cm[Formula: see text]) and FT-Raman (4000–50[Formula: see text]cm[Formula: see text]) observed data. The simulated data along with IR and Raman intensities were calculated using DFT/B3LYP level of theory in combination with 6-311[Formula: see text]G(d,p) basis set. The experimental and theoretical results are found to be in a good agreement with each other. Moreover, thermodynamic properties, molecular electrostatic potential (MEP) and natural bond orbital (NBO) analysis of L-(-)-xylose are also reported. The calculated HOMO and LUMO energies confirm the charge transfer within the molecule.

Density Functional Theory Study on the Complexation of NOTA as a Bifunctional Chelator with Radiometal Ions

1,4,7-Triazacyclononane-1,4,7-triacetic acid (NOTA) is a key bifunctional chelator utilized for the complexation of metal ions in radiopharmaceutical applications; the ability of these chelators depends on the strength of their binding with ions. The focus of the present work is to evaluate the complexation of Cu²⁺, Ga³⁺, Sc³⁺, and In³⁺ radiometal ions with NOTA using density functional theory (B3LYP functional) and 6-311+G(2d,2p)/DGDZVP basis sets. The significant role of ion-water interactions in the chelation interaction energies in solution reflects the competition between ion-water and NOTA-ion interaction in the chelation process. There is reasonable agreement between experimental and theoretical binding constants, geometries, and ¹H NMR chemical shifts. Chelation interaction energies, Gibbs free energies, and entropies in solution show that the NOTA-Ga³⁺ and NOTA-Cu²⁺ are the most and least stable complexes, respectively. The natural atomic charges and second order perturbation analysis reveal charge transfer between NOTA and radiometal ions. The theoretical ¹H NMR chemical shifts of NOTA are in good agreement with experiment; these values are influenced by the presence of the ions, which have a deshielding effect on the protons of NOTA. Global scalar properties such as E_HOMO/E_LUMO, ΔE_LUMO-HOMO, and chemical hardness/softness confirm that the NOTA-Cu²⁺ complex, which has a singly occupied molecular orbital, has the lowest ΔE_LUMO-HOMO value, the least chemical hardness, and the highest chemical softness. The significant variation of the hardness and ΔE_LUMO-HOMO values of the complexes can be attributed to the different positions of the metal ions on the periodic table. This study affirms that, among the radiometal ions, Ga³⁺ can be used to effectively radiolabel NOTA chelator for radiopharmaceutical usage as it binds most stably with NOTA.

The interaction of NOTA as a bifunctional chelator with competitive alkali metal ions: a DFT study

This work investigates NOTA–alkali metal (Li⁺, Na⁺ and K⁺ and Rb⁺) complexation using density functional theory.

Quantum chemical studies on molecular structure, spectroscopic (IR, Raman, UV-Vis), NBO and HOMO-LUMO analysis of 1-benzyl-3-(2-furoyl) thiourea

Vibrational and electronic spectra for 1-benzyl-3-(2-furoyl) thiourea were calculated by using density functional method (B3LYP) with different basis sets. The complete assignment of all vibrational modes was performed on basis of the calculated frequencies and comparing with the reported IR and Raman spectra for that thiourea derivative. UV-visible absorption spectra of the compound dissolved in methanol were recorded and analyzed using time dependent density functional theory (TD-DFT). The calculated values for the geometrical parameters of the title compound are consistent with the ones reported from XRD studies. The stability of the molecule, related to hyper-conjugative interactions, and electron delocalization were evaluated using natural bond orbital (NBO) analysis. Intra-molecular interactions were studied by AIM approach. The HOMO and LUMO analysis are used to determine the charge transfer within the molecule. Molecular electrostatic potential map was performed by the DFT method.

FT-IR, Laser-Raman spectra and computational analysis of 5-Methyl-3-phenylisoxazole-4-carboxylic acid

In this study the experimental and theoretical vibrational frequencies of a newly synthesized anti-tumor, antiviral, hypoglycemic, antifungal and anti-HIV agent namely, 5-Methyl-3-phenylisoxazole-4-carboxylic acid has been investigated. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths, bond angles and torsion angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr and DFT/M06-2X: highly parametrized, empirical exchange correlation function) with 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data and results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated by using the same theoretical calculations.

Molecular structure, vibrational spectral assignments, HOMO-LUMO, MESP, Mulliken analysis and thermodynamic properties of 2,6-xylenol and 2,5-dimethyl cyclohexanol based on DFT calculation

The FT-IR and FT-Raman spectra of 2,6-xylenol and 2,5-dimethyl cyclohexanol are recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1) respectively. The spectral data obtained are assigned to different normal modes by using of comparison with the theoretical values obtained by applying density functional theory (DFT/B3LYP) method with 6-31+G and 6-31++G basis set. The total energy distribution contributions of vibrations modes are distinguished through scaling factors. The calculated HOMO and LUMO energies shows that the charge transfers occur within the molecules. The harmonic frequencies obtained from these two methods are compared. The Mulliken, molecular electrostatic potentials analysis are calculated theoretically.

Vibrational spectroscopic and molecular docking study of 2-Benzylsulfanyl-4-[(4-methylphenyl)-sulfanyl]-6-pentylpyrimidine-5-carbonitrile, a potential chemotherapeutic agent

FT-IR and FT-Raman spectra of 2-Benzylsulfanyl-4-[(4-methylphenyl)-sulfanyl]-6-pentylpyrimidine-5-carbonitrile were recorded and analyzed. The structure of the molecule has been optimized and the structural characteristics have been determined by density functional theory. The geometrical parameters (DFT) are in agreement with the XRD results. HOMO and LUMO and other chemical properties are reported. Nonlinear optical properties are reported. A detailed molecular picture of the title compound and its interactions were obtained from NBO analysis. The negative (red and yellow) regions of the MEP are related to electrophilic reactivity and the positive (blue) regions to nucleophilic reactivity, as shown in the MEP plot and the title compound has several possible sites, CN, N atom of pyrimidine ring and sulfur atoms for electrophilic attack. From the molecular docking studies it is clear that the title compound binds at the catalytic site of the substrate by weak non-covalent interactions most prominent of which are H-bonding, π-π, alkyl-π, and amide-π interactions.

Characterization of 1,5-dimethoxynaphthalene by vibrational spectroscopy (FT-IR and FT-Raman) and density functional theory calculations

In this work, we reported a combined experimental and theoretical study on molecular structure, vibrational spectra and natural bond orbital (NBO) analysis of 1,5-dimethoxynaphthalene. The optimized molecular structure, atomic charges, vibrational frequencies and natural bond orbital analysis of 1,5-dimethoxynaphthalene have been studied by performing DFT/B3LYP/6-31G(d,p) level of theory. The FTIR, FT-Raman spectra were recorded in the region of 4000-400 cm(-1) and 3500-50 cm(-1) respectively. The scaled wavenumbers are compared with the experimental values. The difference between the observed and scaled wavenumber values of the most fundamentals is very small. The formation of hydrogen bond was investigated in terms of the charge density by the NBO analysis. Natural Population Analysis (NPA) was used for charge determination in the title molecule. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis were investigated using theoretical calculations.

Molecular structure, vibrational spectroscopy, NBO and HOMO, LUMO studies of o-methoxybenzonitrile

In the present study, the FT-IR and FT-Raman spectra of o-methoxybenzonitrile (O-MBN) have been recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1), respectively. The fundamental modes of vibrational frequencies of O-MBN are assigned. Theoretical information on the optimized geometry, harmonic vibrational frequencies, infrared and Raman intensities were obtained by means of ab initio Hartree-Fock (HF) and density functional theory (DFT) gradient calculations with complete relaxation in the potential energy surface using 6-311++G(d,p) basis set. The vibrational frequencies which were determined experimentally from the spectral data are compared with those obtained theoretically from ab initio and DFT calculations. A close agreement was achieved between the observed and calculated frequencies by refinement of the scale factors. The infrared and Raman spectra were also predicted from the calculated intensities. Thermodynamic properties like entropy, heat capacity, zero point energy, have been calculated for the molecule. The predicted first hyperpolarizability also shows that the molecule might have a reasonably good non-linear optical (NLO) behavior. The calculated HOMO-LUMO energy gap reveals that charge transfer occurs within the molecule. Stability of the molecule arising from hyper conjugative interactions, charge delocalization have been analyzed using natural bond orbitals (NBO) analysis. Unambiguous vibrational assignment of all the fundamentals was made using the total energy distribution (TED).

Structural, vibrational and electronic characterization of 1-benzyl-3-furoyl-1-phenylthiourea: an experimental and theoretical study

The compound 1-benzyl-3-furoyl-1-phenylthiourea was synthesized and characterized through IR and Raman spectroscopy and its molecular structure was determined.

Theoretical investigations into spectral and non-linear optical properties of brucine and strychnine using density functional theory

The density functional theoretical (DFT) computations were performed at the B3LYP/6-311G++(d, p) level to calculate the equilibrium geometry, vibrational wave numbers, intensities, and various other molecular properties of brucine and strychnine, which were found in satisfactory agreement with the experimental data. The out-of-phase stretching modes of aromatic rings and carbonyl stretching modes in combination with CH stretching modes at stereogenic centers generate VCD signals, which are remarkably efficient configuration markers for these chiral molecular systems. NBOs analysis reveals that the large values of second order perturbation energy (47.24kcal/mol for brucine and 46.93kcal/mol for strychnine) confirms strong hyperconjugative interaction between the orbital containing the lone pair of electron of nitrogen and the neighboring CO antibonding orbital. The molecular electrostatic potential map of strychnine molecule, with no polar groups other than the lone keto group, shows less polarization, which accounts for its lower susceptibility towards electrophilic attack as compared to brucine.