Photophysical and biological aspects of α, β-unsaturated ketones: Experimental and in silico approach

In this work, four fluorinated α, β-unsaturated ketones named as 3-(3-bromophenyl)-1-(3-(trifluoromethyl)phenyl)prop-2-en-1-one (1), 3-(4-methoxyphenyl)-1-(3-(trifluoromethyl)phenyl) prop-2-en-1-one (2), 3-(3-bromo-5-chloro-2-hydroxyphenyl)-1-(3-(trifluoromethyl)phenyl) prop-2-en-1-one (3) and 3-(2-hydroxy-5-methylphenyl)-1-(3-(trifluoromethyl)phenyl)prop-2-en-1-one (4) were synthesized by Claisen-Schmidt reaction. The synthesized molecules were then characterized through ultraviolet-visible spectroscopy (UV-Vis), Fourier transform infrared (FTIR), 1 H-NMR, 13 C-NMR, and mass spectrometry. The antioxidant potential, Urease inhibition, and interaction of compounds 1-4 with Salmon sperm DNA were experimentally explored and supported by molecular docking studies. The synthesized compounds strongly interact with SS-DNA through intercalative mode. It was noticed that compound 1 served as potent Urease inhibitor while compound 4 as better antioxidant among synthesized compounds. Moreover, frontier molecular orbitals, nonlinear optical (NLO) properties, natural bond orbitals, molecular electrostatic potential, natural population analysis, and photophysical properties of synthesized compounds were accomplished through density functional theory and time-dependent density functional theory. The band gap of all the compounds have been worked out using Taucs method. In addition to that, a precise comparative account of UV and IR data obtained from theoretical and experimental findings showed good agreement between theoretical and experimental data. The findings of our studies reflected that compounds 1-4 possess better NLO properties than Urea standard and the band gap data also reflected their prospective use towards optoelectronic materials. The better NLO behavior of compounds was attributed to the noncentrosymmetric structure of synthesized compounds.

A Theoretical Investigation of Novel Sila- and Germa-Spirocyclic Imines and Their Relevance for Electron-Transporting Materials and Drug Discovery

A new class of spirocyclic imines (SCIs) has been theoretically investigated by applying a variety of quantum chemical methods and basis sets. The uniqueness of these compounds is depicted by various peculiarities, e.g., the incidence of planar six-membered rings each with two imine groups (two π bonds) and the incorporation of the isosteres carbon, silicon, or germanium spiro centers. Additional peculiarities of these novel SCIs are mirrored by their three-dimensionality, the simultaneous occurrence of nucleophilic and electrophilic centers, and the cross-hyperconjugative (spiro-conjugation) interactions, which provoke charge mobility along the spirocyclic scaffold. Substitution of SCIs with strong electron-withdrawing substituents, like the cyano group or fluorine, enhances their docking capability and impacts their reactivity and charge mobility. To gain thorough knowledge about the molecular properties of these SCIs, their structures have been optimized and various quantum chemical concepts and models were applied, e.g., full NBO analysis and the frontier molecular orbitals (FMOs) theory (HOMO-LUMO energy gap) and the chemical reactivity descriptors derived from them. For the assessment of the charge density distribution along the SCI framework, additional complementary quantum chemical methods were used, e.g., molecular electrostatic potential (MESP) and Bader's QTAIM. Additionally, using the aromaticity index NICS (nuclear independent chemical shift) and other criteria, it could be shown that the investigated cross-hyperconjugated sila and germa SCIs are spiro-aromatics of the Heilbronner Craig-type Möbius aromaticity.

Development of a GCN-based model to predict in vitro phototoxicity from the chemical structure and HOMO-LUMO gap

The interaction between sunlight and drugs can lead to phototoxicity in patients who have received such drugs. Phototoxicity assessment is a regulatory requirement globally and one of the main toxicity screening steps in the early stages of drug discovery. An in silico-in vitro approach has been utilized mainly for toxicology assessments at these stages. Although several quantitative structure-activity relationship (QSAR) models for phototoxicity have been developed, in silico technology to evaluate phototoxicity has not been well established. In this study, we attempted to develop an artificial intelligence (AI) model to predict the in vitro Neutral Red Uptake Phototoxicity Test results from a chemical structure and its derived information. To accomplish this, we utilized an open-source software library, kMoL. kMoL employs a graph convolutional neural networks (GCN) approach, which allows it to learn the data for the specified chemical structure. kMoL also utilizes the integrated gradient (IG) method, enabling it to visually display the substructures contributing to any positive results. To construct this AI model, we used only the chemical structure as a basis, then added the descriptors and the HOMO-LUMO gap, which was obtained from quantum chemical calculations. As a result, the assortment of chemical structures and the HOMO-LUMO gap produced an AI model with high discrimination performance, and an F1 score of 0.857. Additionally, our AI model could visualize the substructures involved in phototoxicity using the IG method. Our AI model can be applied as a toxicity screening method and could enhance productivity in drug development.

Scalable training of graph convolutional neural networks for fast and accurate predictions of HOMO-LUMO gap in molecules

Graph Convolutional Neural Network (GCNN) is a popular class of deep learning (DL) models in material science to predict material properties from the graph representation of molecular structures. Training an accurate and comprehensive GCNN surrogate for molecular design requires large-scale graph datasets and is usually a time-consuming process. Recent advances in GPUs and distributed computing open a path to reduce the computational cost for GCNN training effectively. However, efficient utilization of high performance computing (HPC) resources for training requires simultaneously optimizing large-scale data management and scalable stochastic batched optimization techniques. In this work, we focus on building GCNN models on HPC systems to predict material properties of millions of molecules. We use HydraGNN, our in-house library for large-scale GCNN training, leveraging distributed data parallelism in PyTorch. We use ADIOS, a high-performance data management framework for efficient storage and reading of large molecular graph data. We perform parallel training on two open-source large-scale graph datasets to build a GCNN predictor for an important quantum property known as the HOMO-LUMO gap. We measure the scalability, accuracy, and convergence of our approach on two DOE supercomputers: the Summit supercomputer at the Oak Ridge Leadership Computing Facility (OLCF) and the Perlmutter system at the National Energy Research Scientific Computing Center (NERSC). We present our experimental results with HydraGNN showing (i) reduction of data loading time up to 4.2 times compared with a conventional method and (ii) linear scaling performance for training up to 1024 GPUs on both Summit and Perlmutter.

Driving the Emission Towards Blue by Controlling the HOMO-LUMO Energy Gap in BF2 -Functionalized 2-(Imidazo[1,5-a]pyridin-3-yl)phenols

Several boron compounds with 2-(imidazo[1,5-a]pyridin-3-yl)phenols, differentiated by the nature of the substituent (R) in the para position of the hydroxy group, have been synthesized and thoroughly characterized both in solution (1 H, 13 C, 11 B, 19 F NMR) and in the solid state (X-ray). All derivatives displayed attractive photophysical properties like very high Stokes shift, high fluorescence quantum yields and a good photostability in solution. Time-Dependent Density Functional Theory (TD-DFT) calculations allowed to define the main electronic transitions as intra ligand transitions (1 ILT), which was corroborated by the Natural Transition Orbitals (NTOs) shapes. The HOMO-LUMO energy gap was correlated to the electronic properties of the substituent R on the phenolic ring, as quantified by its σp Hammett constant.

A Large Starphene Comprising Pentacene Branches

Starphenes are attractive compounds due to their characteristic physicochemical properties that are inherited from acenes, making them interesting compounds for organic electronics and optics. However, the instability and low solubility of larger starphene homologs make their synthesis extremely challenging. Herein, we present a new strategy leading to pristine [16]starphene in preparative scale. Our approach is based on a synthesis of a carbonyl-protected starphene precursor that is thermally converted in a solid-state form to the neat [16]starphene, which is then characterised with a variety of analytical methods, such as ¹³ C CP-MAS NMR, TGA, MS MALDI, UV/Vis and FTIR spectroscopy. Furthermore, high-resolution STM experiments unambiguously confirm its expected structure and reveal a moderate electronic delocalisation between the pentacene arms. Nucleus-independent chemical shifts NICS(1) are also calculated to survey its aromatic character.

Structural and electronic properties of nanosize semiconductor HfSin0/-/2- (n = 6-16) material: a double-hybrid density functional theory investigation

Equilibrium geometries, thermodynamic stabilities, chemical reactivities, and electronic properties of neutral, mono-, and di-anionic Hf-doped silicon nanoclusters HfSi_n^0/-2- (n = 6-16) are calculated by employing an ABCluster global search technique combined with mPW2PLYP scheme. Based on the concordance between simulated and experimental PES, the true global minima are confirmed for n = 6, 9, and 12-16. Optimized geometries for neutral HfSi_n nanoclusters can be divided into three stages: first, Hf atom prefers locating on the surface site of the cluster for n = 6-9, which can be obtained by adding one, two, three, and four Si atoms to HfSi₅ tetragonal bipyramid, respectively (denoted as additive type); then, Hf atom is surrounded by Si atoms with half-cage configuration for n = 10-13; finally, Hf atom is encapsulated into Si cage pattern for n = 14-16. For mono-anions, it is from additive type (n = 6-11) to the cagelike configuration with Hf atom resided in silicon clusters (n = 12-16). For di-anions, it is additive type (n = 6-9) to the Hf-linked configuration (n = 10-11), and in the end to the Hf-encapsulated cagelike motif (n = 12-16). The thorough analysis of stability and chemical bonding revealed that the neutral HfSi₁₆ and di-anionic HfSi₁₅^2- are magic nanoclusters with good thermodynamic and chemical stability, which may make them as the most suitable building block for new functional materials. We suggest that the experimental PES of HfSi_n^- with n = 7, 8, 10, and 11 should be further examined due to the lack of comparably low electron binding energy peaks.

Distortion-Controlled Redshift of Organic Dye Molecules

It is shown, quantum chemically, how structural distortion of an aromatic dye molecule can be leveraged to rationally tune its optoelectronic properties. By using a quantitative Kohn-Sham molecular orbital (KS-MO) approach, in combination with time-dependent DFT (TD-DFT), the influence of various structural and electronic tuning parameters on the HOMO-LUMO gap of a benzenoid model dye have been investigated. These parameters include 1) out-of-plane bending of the aromatic core, 2) bending of the bridge with respect to the core, 3) the nature of the bridge itself, and 4) π-π stacking. The study reveals the coupling of multiple structural distortions as a function of bridge length and number of bridges in benzene to be chiefly responsible for a decreased HOMO-LUMO gap, and consequently, red-shifting of the absorption wavelength associated with the lowest singlet excitation (λ≈560 nm) in the model cyclophane systems. These physical insights together with a rational approach for tuning the oscillator strength were leveraged for the proof-of-concept design of an intense near-infrared (NIR) absorbing cyclophane dye at λ=785 nm. This design may contribute to a new class of distortion-controlled NIR absorbing organic dye molecules.

UV protective heterocyclic disperse azo dyes: Spectral properties, dyeing, potent antibacterial activity on dyed fabric and comparative computational study

Disperse azo dyes are synthesized and characterized by ¹H NMR, ¹³C NMR, LC-MS, Elemental analysis, UV-visible, and fluorescence spectroscopy methods. The azo dyes show absorption maxima in the range of 460-493 nm. Dye with benzothiazole moiety i.e. VM7a and VM8a show a bathochromic shift in absorption maxima of 90 and 26 nm respectively in a polar aprotic solvent (i.e. DMF, DMSO). The dyes show deep red emission in a polar aprotic solvent (i.e. DMF, DMSO) with a Stokes shift of 62 to 180 nm. The dyes are applied on polyester fabric and the dyed fabric exhibit excellent to a good wash and sublimation fastness property. They show a very good UPF rating and almost blocking 95 to 98% of harmful UV radiation. Antibacterial activity of dyed polyester fabric is assessed qualitatively and quantitatively by using AATCC 147 and 100 test method respectively. The dyed fabrics exhibit excellent antibacterial activities against S.aureus (Gram-positive) and K. pneumoniae (Gram-negative). DFT method was used to identify the stable conformer. HOMO-LUMO gap and global reactivity descriptors were calculated using DFT method and correlated with antibacterial activities and light fastness properties respectively.

Data related to conformation dependence of tyrosine binding on the surface of graphene: Bent prefers over parallel orientation

In this data article, M06-2X/6-31G(d) level optimized geometries of complexes of tyrosine conformers binding with graphene sheets are shown in top and side views with selected non-bonding distances. The images of frontier molecular orbitals from HOMO-15 to LUMO+15 of the complexes involving graphene with tyrosine conformers are presented and the isovalue is 0.003 au. For some complexes involving small graphene, the orbitals are from HOMO-5 to LUMO+5. The molecular orbitals highlighted with frames show obvious overlaps between the fragments. Total energies of small and large graphene (G _S and G _L ) and selected tyrosine conformers in gas and aqueous phases obtained at M06-2X/6-31G(d) level are given. The data also include total energies of all complexes in the gas phase and the aqueous phase, binding energies, BSSE (basis set superposition error) correction, and BSSE-corrected binding energies in gas phase and solvation effect on the binding energies obtained at M06-2X/6-31G(d) level. Mulliken charges of tyrosine conformers in gas and aqueous phases, and the deformation energy for tyrosine and graphene in the gas phase complexes are provided. The values of the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO) and HOMO-LUMO energy gaps for some of graphene-tyrosine complexes that were not reported in the article [1] are given. The data is related to the research article "Conformation dependence of tyrosine binding on the surface of graphene: Bent prefers over parallel orientation" [1].

Study on Structural Evolution, Thermochemistry and Electron Affinity of Neutral, Mono- and Di-Anionic Zirconium-Doped Silicon Clusters ZrSin0/-/2- (n = 6-16)

We have carried out a global search of systematic isomers for the lowest energy of neutral and Zintl anionic Zr-doped Si clusters ZrSi_n^0/-/2- (n = 6–16) by employing the ABCluster global search method combined with the mPW2PLYP double-hybrid density functional. In terms of the evaluated energies, adiabatic electron affinities, vertical detachment energies, and agreement between simulated and experimental photoelectron spectroscopy, the true global minimal structures are confirmed. The results reveal that structural evolution patterns for neutral ZrSi_n clusters prefer the attaching type (n = 6–9) to the half-cage motif (n = 10–13), and finally to a Zr-encapsulated configuration with a Zr atom centered in a Si cage (n = 14–16). For Zintl mono- and di-anionic ZrSi_n^-/2-, their growth patterns adopt the attaching configuration (n = 6–11) to encapsulated shape (n = 12–16). The further analyses of stability and chemical bonding make it known that two extra electrons not only perfect the structure of ZrSi₁₅ but also improve its chemical and thermodynamic stability, making it the most suitable building block for novel multi-functional nanomaterials.

Computational investigation of double nitrogen doping on graphene

Density functional theory (DFT) calculations were performed to study doping of two nitrogen atoms at different positions on a finite-sized graphene model of C₈₂H₂₄. We examined 21 structures of double nitrogen doped graphene to calculate their relative stabilities. The structure with two nitrogen atoms located apart is the most stable among the positional isomers considered in this study. For double nitrogen doping within a six-membered ring, the 1,4-position is more preferred than 1,3- or 1,2-positions for the finite-sized single layer graphene sheet. Our computational study supports the experimental observation of two nitrogen atoms at the 1,3- and 1,4-positions in a single six-membered ring of graphene. Furthermore, the structures with N-N bond are the least stable among two nitrogen doped graphene structures. The effects of nitrogen doping and the positions of two nitrogen atoms on the HOMO-LUMO energy gap of pristine graphene were analyzed.

Design, Synthesis, Characterization and Electrochemical Properties of BODIPY Dyes Containing Mono, Bis-2-Naphthyloxyhexyloxy and 4-(Benzyloxy)Phenoxyhexyloxy Groups

In this study, the synthesis of boron dipyrromethene dyes containing mono, bis-2-naphthyloxyhexyloxy and 4-(benzyloxy)phenoxyhexyloxy groups has been reported. Boron dipyrromethene dyes were synthesized from the mono, bis-benzaldehyde derivatives with 2,4-dimethylpyrrole in dichloromethane in the presence of trifluoroacetic, 2,3-dichloro-5,6-dicyano-p-benzoquinon, triethyl amine and boron trifluoride diethyl etherate, respectively. Electrochemical characterization of boron dipyrromethene dyes were carried out with voltammetric measurements. Electrochemical studies show that boron dipyrromethene dyes containing mono, bis-2-naphthyloxyhexyloxy and 4-(benzyloxy)phenoxyhexyloxy groups have reversible one reduction potentials unlike irreversible one oxidation potentials. Graphical Abstract ᅟ.

Optical Absorption Spectra and Electronic Properties of Symmetric and Asymmetric Squaraine Dyes for Use in DSSC Solar Cells: DFT and TD-DFT Studies

The electronic absorption spectra, ground-state geometries and electronic structures of symmetric and asymmetric squaraine dyes (SQD1–SQD4) were investigated using density functional theory (DFT) and time-dependent (TD-DFT) density functional theory at the B3LYP/6-311++G** level. The calculated ground-state geometries reveal pronounced conjugation in these dyes. Long-range corrected time dependent density functionals Perdew, Burke and Ernzerhof (PBE, PBE1PBE (PBE0)), and the exchange functional of Tao, Perdew, Staroverov, and Scuseria (TPSSh) with 6-311++G** basis set were employed to examine optical absorption properties. In an extensive comparison between the optical data and DFT benchmark calculations, the BEP functional with 6-311++G** basis set was found to be the most appropriate in describing the electronic absorption spectra. The calculated energy values of lowest unoccupied molecular orbitals (LUMO) were 3.41, 3.19, 3.38 and 3.23 eV for SQD1, SQD2, SQD3, and SQD4, respectively. These values lie above the LUMO energy (−4.26 eV) of the conduction band of TiO₂ nanoparticles indicating possible electron injection from the excited dyes to the conduction band of the TiO₂ in dye-sensitized solar cells (DSSCs). Also, aromaticity computation for these dyes are in good agreement with the data obtained optically and geometrically with SQD4 as the highest aromatic structure. Based on the optimized molecular geometries, relative positions of the frontier orbitals, and the absorption maxima, we propose that these dyes are suitable components of photovoltaic DSSC devices.

Density functional theory investigation of opto-electronic properties of thieno[3,4-b]thiophene and benzodithiophene polymer and derivatives and their applications in solar cell

PTBs polymers with thieno[3,4-b]thiophene [TT] and benzodithiophene [BDT] units have particular properties, which demonstrate it as one of the best group of donor materials in organic solar cells. In the present work, density functional theory (DFT) is applied to investigate the optimized structure, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), band gap and dihedral angle of PTB7 at B3LYP/6-31G(d). Two different approaches are applied to carry out these investigations: Oligomer extrapolation technique and periodic boundary condition (PBC) method. The results obtained from PBC-DFT method are in fair agreement with experiments. Based on these reliable outcomes; the investigations continued to perform some derivatives of PTB7. In this study, sulfur is substituted by nitrogen, oxygen, silicon, phosphor or selenium atoms in pristine PTB7. Due to the shift of HOMO and LUMO levels, smaller band gaps are predicted to appear in some derivatives in comparison with PTB7. Maximum theoretical efficiencies, η, of the mentioned derivatives as well as local difference of dipole moments between the ground and excited states (Δμge) are computed. The results indicate that substitution of sulfur by nitrogen or oxygen in BDT unit, and silicon or phosphor in TT unit of pristine PTB7 leads to a higher η as well as Δμge.