Highest Occupied Molecular Orbital-lowest Unoccupied Molecular Orbital Research Articles

Theoretical Investigation and Design of Bioactive Quinoline Derivatives as Inhibitors of DNA Gyrase of Salmonella typhi

The ever-increasing rate of resistance to existing antibiotics by Salmonella typhi has made the search for novel drug candidates a necessity. In this study, Molecular docking technique was used to screen 18 bioactive quinoline derivatives against DNA gyrase of Salmonella typhi using PyRx graphical user interface of AutoDock Vina software. Ligand with the best binding affinity against the target macromolecule was used as prototype to design novel analogues with enhanced potencies. With the aid of Swiss ADME online server and Osiris DataWarrior v5.5.0 programme, the absorption, distribution, metabolism, excretion and toxicity (ADMET) profiles of the ligands were evaluated and their electronic properties were computed using density functional theory (DFT) method of Spartan 14.0 software. Ligand 3 (L3) with the best binding affinity (TG) value of −10.5 kcal/mol was chosen as a prototype to design La and Lb with TG value of −10.7 kcal/mol and −10.8 kcal/mol; binding constant (ka) of 7.04 × 107 and 8.35 × 107 ; and dissociation constant (kd) of 1.42 x 10−8 and 1.2 × 10−8, respectively. When compared with ciprofloxacin (TG = −7.7 kcal/mol), the ligands could be more potent. Likewise, the ligands were found to possess excellent oral bioavailability and pharmacokinetic profiles. Furthermore, DFT calculations on La and Lb revealed that they possess highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energy gap of 3.46 eV and 3.45 eV; and global electrophilicity index of 3.83 eV and 3.96 eV, respectively. The designed ligands tend to be consistent with all the validation protocols deployed in this study and as such could be recommended as novel drug candidates for treatment of Salmonella typhi induced salmonellosis.

Thiadiazole/Thiadiazine Derivatives as Insecticidal Agent: Design, Synthesis, and Biological Assessment of 1,3,4-(Thiadiazine/Thiadiazole)-Benzenesulfonamide Derivatives as IGRs Analogues against Spodoptera littoralis.

In keeping with our investigation, a simple and practical synthesis of novel heterocyclic compounds with a sulfamoyl moiety that can be employed as insecticidal agents was reported. The compound 2-hydrazinyl-N-(4-sulfamoylphenyl)-2-thioxoacetamide 1 was coupled smoothly with triethylorthoformate or a variety of halo compounds, namely phenacyl chloride, chloroacetyl chloride, chloroacetaldehyde, chloroacetone, 1,3-dichloropropane, 1,2-dichloroethane, ethyl chloroformate, 2,3-dichloro-1,4-naphthoquinone, and chloroanil respectively, which afforded the 1,3,4-thiadiazole and 1,3,4-thiadiazine derivatives. The new products structure was determined using elemental and spectral analysis. Under laboratory conditions, the biological and toxicological effects of the synthetic compounds were also evaluated as insecticides against Spodoptera littoralis (Boisd.). Compounds 3 and 5 had LC50 values of 6.42 and 6.90 mg/L, respectively. The investigated compounds (from 2 to 11) had been undergoing molecular docking investigation for prediction of the optimal arrangement and strength of binding between the ligand (herein, the investigated compounds (from 2 to 11)) and a receptor (herein, the 2CH5) molecule. The binding affinity within docking score (S, kcal/mol) ranged between -8.23 (for compound 5), -8.12 (for compound 3) and -8.03 (for compound 9) to -6.01 (for compound 8). These compounds were shown to have a variety of binding interactions within the 2CH5 active site, as evidenced by protein-ligand docking configurations. This study gives evidence that those compounds have 2CH5-inhibitory capabilities and hence may be used for 2CH5-targeting development. Furthermore, the three top-ranked compounds (5, 3, and 9) and the standard buprofezin were subjected to density functional theory (DFT) analysis. The highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energy difference (ΔE) of compounds 5, 3, and 9 was found to be comparable to that of buprofezin. These findings highlighted the potential and relevance of charge transfer at the molecular level.

Hydrogen Storage Capacity of Cobalt Cluster Ions.

The adsorption of H2 on gas-phase Con± (n = 5-12) clusters at 300 K and the desorption of H2 from ConHm± upon heating were studied experimentally by combining thermal desorption spectrometry and mass spectrometry to elucidate the hydrogen storage property of the Co clusters. Hydrogen atoms adsorbed well on Con+ (n = 5, 10-12) and Con- (n = 5-12) at 300 K to form ConHm±. The atomic ratios, m/n, for ConHm- (0.9-1.4) were higher than those for ConHm+ (0.2-1.1). According to density functional theory (DFT) calculations, the first few H2 molecules had a tendency to dissociatively adsorb onto the Co clusters. Further, the bonding nature of the H atoms was ionic, similar to the H atoms in the metallic hydrides. In contrast, H2, adsorbed molecularly, was explained in terms of σ complex formation. H2 molecules were desorbed from the clusters upon heating. The temperature dependences showed that ConHm- released H2 at a higher temperature (700-800 K) than ConHm+ (600-700 K), suggesting that Con- should have a higher affinity to hydrogen than Con+. The desorption temperatures were lower than those of VnHm+, which was consistent with the fact that the adsorption energies of H2 were lower for the Co clusters than those for the V clusters. The low adsorption energies were ascribed to their large highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gaps in the Co clusters.

Theoretical investigation of the conformational preference and spectroscopic analysis of cinnamoyl chloride and cinnamide

The rotational isomers of cinnamoyl chloride and cinnamide have been computed using the B3LYP method and the 6-311++G (d, p) basis set to calculate their molecular structure, conformational stability, and spectroscopic properties. Computations revealed that the s-cis rotamers of both compounds are the most stable rotamers in both the gas phase and in the solution. The s-trans rotational barrier is 8.76 kcal/mol and 5.63 kcal/mol for cinnamoyl chloride and cinnamide, respectively. Replacing the Cl group of the cinnamoyl chloride with the NH2 group in the cinnamide has reduced the highest occupied molecular orbital – lowest unoccupied molecular orbital (HOMO-LUMO) gap. The solvation effects on the conformational stability of rotamers have been studied in nine solvents (heptane, chloroform, tetrahydrofuran, dichloroethane, acetone, ethanol, methanol, dimethyl sulfoxide, and water) using the integral equation formalism of the polarizable continuum model. The chemical shifts of 13C and 1H NMR spectra have been simulated in the gas phase, dimethyl sulfoxide (DMSO), and chloroform using the gauge-independent atomic orbital (GIAO) method. The UV absorption spectral analysis has been computed in different solvents (chloroform, methanol, and water), and atomic charges calculated. The examination of vibrational wave numbers and their corresponding assignments revealed excellent agreement between simulated and experimental infrared spectra for the studied molecules.

Strategies to Improve the Quantum Computation Accuracy for Electrochemical Windows of Ionic Liquids.

Rational design of ionic liquids (ILs) with wide electrochemical windows (ECWs) for high-voltage cathodes is essential to elevating the energy density of current rechargeable batteries. It is significant to determine appropriate strategies for accurately predicting the ECWs of ILs. In this study, we compare the calculated ECWs based on three quantum methods, including the highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) method, the ionization potential-electron affinity (IP-EA) method, and the thermodynamic method, under four unique combinations of simulation environments, and assess the discrepancies between the calculated and the experimental results of ECWs. For the three quantum methods, although HOMO-LUMO and IP-EA methods show limited prediction accuracy compared to the experimental values, they can qualitatively rank the anodic limits of anions and the cathodic limits of cations. For the thermodynamic method, we demonstrate that the highest accuracy can be achieved by considering the most rational redox reaction process. By varying the calculation environments, the calculated ECWs tend to be underestimated by considering separate cations and anions of ILs under gas phase, whereas they always exhibit overestimated results when calculating based on the cation-anion pairs. When the computation considers isolated ions with the solvent model plus proper thermodynamic corrections, we observe improved consistency with the experimental results. Though all methods have limitations to achieving perfect predictions of ECWs, we believe rational selection of calculation methods based on application-oriented scenarios can balance the efficiency and accuracy of the results for the development of a high-throughput and accurate database of ECWs for ILs.

Superacidic Properties of Protonated PtFn (n = 1–6) and Their Ability to Form Supersalts: DFT Study

AbstractIn the present communication, this study has modeled protonated PtFn (n = 1–6), a new series of superacids. The calculated vertical de‐attachment energy (VDE) of PtFn (n = 1–6) reestablishes the superhalogenic behavior. The vibrational frequency, dissociation energy through the HF channel, and optimized geometries are utilized to discuss the stability of HPtFn (n = 1–6). The deprotonation energy of HPtFn is used to calculate the acidic strength of HPtFn (n = 1–6). The acidity of protonated PtFn (n = 1–6) is directly related to its counterpart superhalogen anions. The computed correlation factor (R2 = 0.9754) shows that VDE is directly associated with acidity. The mechanism of acidity of HPtFn (n = 1–6) is described by using natural bond orbital analysis charges on atoms. The electronic properties of HPtFn (n = 1–6) are calculated using the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy. The nature of chemical reactivity is also determined by the HOMO–LUMO plot of HPtFn (n = 1–6). It has formed the supersalts using superacids HPtFn (n = 1–6) and superbase (OLi3OH), and the nature of supersalts is compared with traditional salt LiF. The most stable conformers of supersalts PtFnOLi3 (n = 2–6) are analyzed for optoelectronic properties. It has computed the dissociation of supersalts through neutral and anions through superhalogns and superalkalis. The computed results show that PtF4OLi3 favors dissociation through anions as in traditional salts. The nonlinear optical parameters are calculated using dipole moment, mean polarizability, anisotropic polarizability, molar reflectivity (MR), order parameters, and hyperpolarizability of PtFnOLi3 (n = 2–4). The estimated nonlinear optical properties parameters are compared with corresponding parameters of traditional salt LiF by the same level theory.

Hybrid DFT Geometries and Properties for 17k Lanthanoid Complexes─The LnQM Data Set.

The unique properties of lanthanoids and their diverse applications make them an indispensable part of modern research and industry. While the field has garnered attention, there remains a gap in available molecule data sets that facilitate both classical quantum chemistry calculations and the burgeoning field of machine learning in data science applications. This research addresses the need for a comprehensive data set that allows for a comparative analysis of various lanthanoids. The herein presented, curated data set includes 17269 monolanthanoid complexes derived from 1205 distinct ligand motifs. Structures encompass all 15 lanthanoids in the +3 oxidation state and exhibit molecular charges ranging from -1 to +3, including structures with a high spin multiplicity up to 8. Starting from lanthanum complexes, samples were processed with a permutation of the central lanthanoid atom, resulting in highly comparable subsets, facilitating comparative studies in which the influence of the lanthanoid can be investigated independently of ligand effects. The data set provides a broad range of features such as PBE0-D4/def2-SVP optimized geometries and optimization trajectories, while also covering ωB97M-V/def2-SVPD energies, rotational constants, dipole moments, highest occupied molecular orbital-lowest-unoccupied molecular orbital (HOMO-LUMO) energies, and Mulliken, Löwdin, and Hirshfeld population analyses. Additionally, coordination numbers, polarizabilities, and partial charges from D4, electronegativity equilibration (EEQ), GFN2-xTB, and charge extended Hückel (CEH) calculations are included. The data set is openly accessible and may serve as a basis for further investigations into the properties of lanthanoids.

Synthesis, structure, growth, characterization and quantum chemical studies on 2-amino-5-bromopyridinium trichloroacetate: A novel phasematchable organic NLO single crystal

Organic crystals have become excellent candidates towards nonlinear optical (NLO) applications as they possess superior second and third order optical nonlinearities and high electro-optic coefficients when compared with their inorganic counterparts. In this direction, 2-Amino-5-bromopyridinium trichloroacetate (2A5BPT), a new organic second-order nonlinear optical compound is synthesized and optical grade single crystals are formed utilizing a slow evaporation solution growth approach at room temperature while using methanol as the solvent. Single crystal X-ray diffraction study shows that the title compound is assigned to monoclinic crystal system having non-centrosymmetric space group Cc. The crystal is transparent ( ̴ 85%) throughout the whole visible spectrum, according to the Ultraviolet-Visble (UV–Vis) spectra, with a cutoff wavelength of 367 nm and an optical energy band gap Eg of 3.32 eV. The crystal possesses good thermal stability. The compound has a 1.6 times greater powder second harmonic generation (SHG) efficiency than potassium dihydrogen phosphate (KDP). The phase matchability of the 2A5BPT is studied through particle size dependence of SHG. The intermolecular connection demonstrated by numerous inter contacts has been shown by a molecular Hirshfeld surface analysis of the crystal structure, and the related 2-dimensional finger print analysis further evaluates the individual contribution from each atom. In order to examine the first order hyperpolarizability, molecular electrostatic potential, and Highest occupied molecular orbital-Lowest unoccupied molecular orbital (HOMO-LUMO) energies, the quantum chemical calculations for the title molecule (2A5BPT) were carried out by density functional theory (DFT) utilizing the B3LYP/6–311++G(d,p) basis set. According to these results, the 2A5BPT crystal could be suitable for optoelectronic applications.

Molecular Structure, Geometry Properties, HOMO-LUMO, and MEP Analysis of Acrylic Acid Based on DFT Calculations

In this paper, quantum computational chemistry methods were employed to calculate the molecular properties of acyrilic acid. The molecule was optimized at STO-3G basis set using Density Functional Theory (DFT/B3LYP). The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels of the frontier orbitals were obtained using DFT. The energy gap of HOMO–LUMO orbitals has been found to be 5.545 eV. Molecular Electrostatic Potential (MEP) surface analyses were also investigated. In addition, the basic crystal structure properties of acrylic acid were shown via the Crystallographic Information File (CIF). A discussion of the fundamental theory was reported behind the characterization methods.

New homoleptic imine derivative of lawsone and its metal complexes: Preparation, characterization, in vitro and in silico biological investigation

In this article, a Schiff base derivative has been prepared using 2‐hydroxy‐1,4‐naphthoquinone and 3‐amino‐1,2,4‐triazole, and consecutively, four metal complexes (Co(II), Ni(II), Cu(II) and Zn(II)) have been synthesized using this Schiff base derivative as precursor ligand. Characterization of the synthesized compounds are done by employing spectral techniques such as UV–vis, infrared (IR), nuclear magnetic resonance (NMR), mass and electron paramagnetic resonance (EPR). All these methods establish the existence of imine group and the octahedral geometry of the complexes. The synthesized complexes are evaluated for their DNA binding properties that confirm that the binding mode is intercalation. The bioactive ligand and its complexes also exhibit pronounced pharmacological activities such as antioxidant and antimicrobial activities against bacteria such as Bacillus subtilis, Staphylococcus aureus, Escherichia coli and Salmonella typhi; fungi, namely, Aspergillus niger, Aspergillus flavus, Candida albicans and Rhizoctonia bataticola. Moreover, the compounds are examined for their density functional theory (DFT) studies using Gaussian 09 programme. Various reactivity descriptors are calculated based on the highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO‐LUMO) energies. Molecular docking is conducted with two different receptors 1BNA and 1HD2 proteins to get a wide knowledge on the in vitro biological examination and also the interaction of the compounds with different proteins.

Ag3PO4/Bi2WO6 Heterojunction Photocatalyst with Remarkable Visible-Light-Driven Catalytic Activity

Novel Ag3PO4/Bi2WO6 catalysts with enhanced visible-light performance were synthesized using a hydrothermal method and characterized to investigate their morphology, microscopic structure, and binding energies. Photoluminescence spectrum (PL) and electrochemical impedance spectroscopy (EIS) data demonstrate that the formed Ag3PO4/Bi2WO6 heterojunction effectively promotes hole (h+)–electron (e−) separation and transfer efficiency, resulting in the enhancement of photocatalytic activity. Ag3PO4/Bi2WO6 displays higher photocatalytic activity than pure Bi2WO6 or Ag3PO4 alone. Photogenerated holes (h+), ·O2−, and ·OH were found to be the main active species for the degradation of malachite green (MG), methylene blue (MB), and Rhodamine B (RhB). The DFT calculation explains the photostability of Ag3PO4/Bi2WO6 from the perspective of electronic structure. The bandgap of Ag3PO4/Bi2WO6 between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) is 1.41 eV, compared with that of Ag3PO4 at 0.91 eV and Bi2WO6 at 2.59 eV. Ag–O–Bi hybridization and the wide HOMO–LUMO bandgap lead to difficulty in electron transfer. As a consequence, Ag+ is difficult to obtain electrons and difficult to convert into Ag0, which makes the catalyst stable.

Role of Spin Polarization and Dynamic Correlation in Singlet-Triplet Gap Inversion of Heptazine Derivatives.

The new generation of proposed light-emitting molecules for organic light-emitting diodes (OLEDs) has raised considerable research interest due to its exceptional feature─a negative singlet-triplet (ST) gap violating Hund's multiplicity rule in the excited S1 and T1 states. We investigate the role of spin polarization in the mechanism of ST gap inversion. Spin polarization is associated with doubly excited determinants of certain types, whose presence in the wave function expansion favors the energy of the singlet state more than that of the triplet. Using a perturbation theory-based model for spin polarization, we propose a simple descriptor for prescreening of candidate molecules with negative ST gaps and prove its usefulness for heptazine-type molecules. Numerical results show that the quantitative effect of spin polarization decreases linearly with the increasing highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) exchange integral. Comparison of single- and multireference coupled-cluster predictions of ST gaps shows that the former methods provide good accuracy by correctly balancing the effects of doubly excited determinants and dynamic correlation. We also show that accurate ST gaps may be obtained using a complete active space model supplemented with dynamic correlation from multireference adiabatic connection theory.

Theoretical Perspective toward Designing of 5-Methylbenzo [1,2-b:3,4-b':6,5-b″] trithiophene-Based Nonlinear Optical Compounds with Extended Acceptors.

A series of benzotrithiophene-based compounds (DCTM1-DCTM6) having D1-π1-D2-π2-A configuration were designed using a reference molecule (DCTMR) via incorporating pyrrole rings (n = 1-5) as the π-spacer (π2). Quantum chemical calculations were performed to determine the impact of the pyrrole ring on the nonlinear optical (NLO) behavior of the above-mentioned chromophores. The optoelectronic properties of the compounds were determined at the MW1PW91/6-311G(d,p) functional. Among all of the derivatives, DCTM5 exhibited the least highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) band gap (Eg) 0.968 eV with a high softness of 0.562 eV-1, and hence possessed the highest polarizability. Interestingly, transition density matrix (TDM) findings demonstrated that DCTM5 with an effective diagonal charge transmission proportion at the acceptor group supports the frontier molecular orbital (FMO) results. Additionally, the exciton binding energy values for DCTM1-DCTM6 were found to be less than that for DCTMR and thus, the effective charge transfer was examined in the derivatives. All of the derivatives exhibited effective NLO outcomes with the highest magnitude of linear polarizability ⟨α⟩, and first (βtot) and second (γtot) hyperpolarizabilities relative to the parent compound. Nevertheless, the highest βtot and γtot were obtained for DTCM1 and DTCM6, 7.0440 × 10-27 and 22.260 × 10-34 esu, respectively. Hence, through this structural tailoring with a pyrrole spacer, effective NLO materials can be obtained for optoelectronic applications.

Effect of solvent role in electronic properties, band gap, electron injection barrier, charge transport nature, topology studies (ELF, LOL, RDG), and optical properties of azoles for multifunctional applications

The ground state geometries of oxazole compounds, i.e., 3,5-Bis-(4-chloro-phenyl)-7a-methyl-dihydro-oxazolo[3,4-c]oxazole (Compound1) and 3,5-Bis-(4-methoxy-phenyl)-7a-methyl-dihydro-oxazolo[3,4-c]oxazole (Compound2) were optimized using Density functional theory employing B3LYP/6-31G++ level for comparing the geometric parameters (torsion angles, bond angles & bond lengths) with the X-ray crystallographic information. We explored the charge transport nature, wave functional properties, optical and electronic properties of both the oxazoles. The computed geometric parameters are rational to the experimental data. The time-domain TD - B3LYP/6-31G++ & the B3LYP/6-31G++ levels were used to reveal the electronic characteristics and absorption wavelength. Intra-molecular charge transfer was perceived in studied compounds. The IEFPCM (Integral Equation Formalism Polarizable Continuum Model) model was used to calculate the solvation UV spectrum. The effect of various solvents (acetone, acetonitrile, DMF(Dimethylformamide), DMSO (Dimethyl sulfoxide) and methanol) was examined on the excitation energies but solvent polarity has no discernible impact on the wavelengths of absorption. From HOMO-LUMO (Highest Occupied Molecular Orbital – Lowest Unoccupied Molecular Orbital) orbitals with various solvent molecules, band gap energies with the solvation effect are determined. Additionally, through the use of topological analytics like RDG (Reduced Density Gradient), ELF (Electron Localisation Function) & LOL (Localised Orbital Locator), the energy concentration of electrons was elucidated. Furthermore, the outcome of electron-donating cluster (–OCH3) and electron-withdrawing cluster (–Cl) was studied on open-circuit voltage, bandgap alignment, electron coupling constants, excitons dissociation values, ΔGinject – electron injection, LHE-Light Harvesting Efficiency and electron coupling constants (|VRP|).

Significance of anchoring group design on light harvesting efficiency of dye-sensitized solar cells and non-linear optical response

Dye-sensitizers designed from coumarin backbone are widely utilized in solar light harvesting due to their versatile performance in dye-sensitized solar cells (DSSC). They are well-known as non-linear optical (NLO) materials. In this case study, we have designed coumarin-based sensitizers containing thiophene as a common spacer with the different acceptor-anchoring groups, ethyl-2-cyanoacrylate (SPDSSC 1) and 2-cyanoacrylic acid (SPDSSC 2). Density functional theory (DFT) and time-dependent- DFT (TD-DFT) computational calculations of these molecules predict superior light harvesting capability and NLO properties. The calculated HOMO–LUMO energy gap of these dyes showed an inverse relation with chemical potential and electrophilicity index and was directly related to hardness and hyperhardness. It was also seen β0 and γ and PCE follow a similar trend. Further, computations of sensitizers@TiO2 indicated sensitizers with ethyl-2-cyanoacrylate bonded with TiO2 cluster via unidentate linkage, whereas 2-cyanoacrylic acid containing sensitizer involved bidentate bonding with TiO2. Apart from this, sensitizers with 2-cyanoacrylic acid anchors showed much planer geometry. Also, the quantitative analysis of the highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) and MEP plots showed that more electron clouds shifted to the TiO2 cluster in the sensitizer with 2-cyanoacrylic acid (SPDSSC 2) than ethyl-2-cyanoacrylate (SPDSSC 1). Further, both molecules were taken as sensitizers in the DSSC device. SPDSSC 2 showed higher power conversion efficiency than SPDSSC 1. Overall, results disclosed that sensitizers with ethyl-2-cyanoacrylate having two oxygen atoms in their anchoring part could bind with only carbonyl oxygen. And this monodentate binding of ethyl-2-cyanoacrylate with TiO2 leads to poor charge transfer in the semiconductor's conduction band, resulting in poor DSSC performance.

Interpretable Fragment‐Based Molecule Design with Self‐Learning Entropic Population Annealing

Self‐learning entropic population annealing (SLEPA) is a recently developed method used for achieving interpretable black‐box optimization via density‐of‐states estimation. Applying SLEPA to a chemical space is not straightforward, however, because of its dependence on Markov chain Monte Carlo sampling in the space of generated entities. Herein, SLEPA is applied to optimal molecule generation by combining an irreducible Markov chain in the space of fragment multisets and a probabilistic fragment assembler such as MoLeR. The weighted samples from SLEPA are used to identify salient fragments for the highest occupied molecular orbitals‐lowest unoccupied molecular orbitals (HOMO‐LUMO) gap maximization and minimization, and the relationship between the identified fragments and the electronic structures is elucidated. This approach offers a viable platform to reconcile the incompatible goals of optimization and interpretation during molecular design.

Calculation of the one- and two-photon absorption spectra of water-soluble stilbene derivatives using a multiscale QM/MM approach.

We calculated the one- (OPA) and two-photon absorption (TPA) spectra of two large water-soluble stilbene derivatives presenting TPA cross sections of about 400 GM. However, the reported experimental TPA spectra present a spectral gap region, and a theoretical study of these promising molecules seems now timely and relevant. These molecules are composed of 200 or more atoms, becoming a challenge to obtain the TPA spectra even using density functional theory at the time-dependent quadratic response formalism. Thus, both OPA and TPA were also calculated using the INDO-S semi-empirical method. We used explicit solvent molecules using the sequential-quantum mechanics/molecular mechanics to include the solvent effects. Our results show that different transitions are participating in the OPA and TPA processes and that exchange-correlation functionals, including larger Hartree-Fock contributions, provide a better description of the OPA spectra; however, the opposite trend is observed on the TPA spectra. Alternatively, INDO-S/CISD, including contributions from single and double excitations, systematically describes both OPA and TPA bands with similar shifts and better reproduces the relative intensities of the two TPA bands compared to the experimental ones. The OPA spectra are characterized by a Highest Occupied Molecular Orbital-Lowest Unoccupied Molecular Orbital (HOMO-LUMO) excitation, while the low-energy TPA band is ascribed to a single transition encompassing the (HOMO-1)-LUMO and HOMO-(LUMO+1) excitations and the high-energy one is a combination of several transitions. Thus, although more studies are required to better assess the capability of the INDO-S/CISD method in describing the TPA spectra of large molecules, our results corroborate that it is a promising alternative.

Synthesis of New Derivatives of Benzylidinemalononitrile and Ethyl 2-Cyano-3-phenylacrylate: In Silico Anticancer Evaluation.

In this study, microwave-assisted Knoevenagel condensation was used to produce two novel series of derivatives (1-6) from benzylidenemalononitrile and ethyl 2-cyano-3-phenylacrylate. The synthesized compounds were characterized using Fourier transform infrared (FT-IR) and 1H NMR spectroscopies. The pharmacodynamics, toxicity profiles, and biological activities of the compounds were evaluated through an in silico study using prediction of activity spectra for substances (PASS) and Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) studies. According to the PASS prediction results, compounds 1-6 showed greater antineoplastic potency for breast cancer than other types of cancer. Molecular docking was employed to investigate the binding mode and interaction sites of the derivatives (1-6) with three human cancer targets (HER2, EGFR, and human FPPS), and the protein-ligand interactions of these derivatives were compared to those reference standards Tyrphostin 1 (AG9) and Tyrphostin 23 (A23). Compound 3 showed a stronger effect on two cell lines (HER2 and FPPS) than the reference drugs. A 20 ns molecular dynamics (MD) simulation was also conducted to examine the ligand's behavior at the active binding site of the modeled protein, utilizing the lowest docking energy obtained from the molecular docking study. Enthalpies (ΔH), Gibbs free energies (ΔG), entropies (ΔS), and frontier molecular orbital parameters (highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap, hardness, and softness) were calculated to confirm the thermodynamic stability of all derivatives. The consistent results obtained from the in silico studies suggest that compound 3 has potential as a new anticancer and antiparasitic drug. Further research is required to validate its efficacy.

Density functional theory studies on molecular structure, vibrational spectra, AIM, HOMO-LUMO, electronic properties, and NBO analysis of benzoic acid monomer and dimer

In this study, the molecular structure, vibrational frequencies, and atom-in-molecule (AIM) analysis of the benzoic acid monomer and dimer were investigated. Geometry optimization and vibrational frequency calculations for the monomer and dimer were carried out at the density functional theory (DFT) level with the 6-311++G(2d,p) basis set. UV-Vis spectroscopy and electronic properties (i.e., excitation energies, oscillator strengths) were calculated by time-dependent DFT (TD-DFT) in different solvents. The calculated absorption values mainly represented excitation from HOMO-1 (H-1)  LUMO and HOMO  LUMO+2 (L+2). The structure-activity relationship was interpreted by its molecular electrostatic potential (MEP) surface, which is very useful to the research of molecular structures and their physiochemical-property relationships. The highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energy was analysed. The HOMO-LUMO energy gap and other related molecular properties were also calculated. In addition, natural bond orbital (NBO) analysis was carried out to investigate the various intra-intermolecular interactions in the molecular system.

Equilibrium configurations and electronic structure of fullerene ultrathin films on SrTiO3(0 0 1) surface

Ultrathin fullerene (C60) films on various metal and semiconductor substrates have been intensively studied but not yet on a perovskite oxide substrate. Using scanning tunneling microscopy and spectroscopy, we investigated the molecular arrangement and electronic structure of C60 ultrathin films grown on a SrTiO3(001) surface. Subject to strong coupling and weak screening from the substrate, the monolayer C60 exhibit short-range ordered molecular arrangement with disordered molecular orientation and a substantially large highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap (∼4.1 eV). In contrast, C60 in the 2nd and 3rd layers are self-assembled into hexagon lattices with a quasi-(2 × 2) superstructure resulted from the arrangement of molecular orientations showing a chiral pinwheel structure. The HOMO-LUMO gap of the multi-layer C60 further expands to ∼ 4.6 eV, very close to that of gas-phase C60, indicating a negligible inter-layer screening effect.