Molecular Electronic Spectra Research Articles

Theoretical Prediction and Comprehensive Characterization of an All-Nitrogenatomic Ring, Cyclo[18]Nitrogen (N18).

The cyclic molecule cyclo[18]carbon composed of 18 carbon atoms has been observed in condensed phase experiment in recent years and has attracted great attention. Through state-of-art quantum chemistry calculation, this study found that 18 nitrogen atoms can also form a macrocyclic system, cyclo[18]nitrogen (N18), though its lifetime is very short at room temperature and can only exist for a relatively long time at very low temperatures. We comprehensively theoretically studied properties of N18, including geometric configurations, thermal decomposition mechanism and rate, molecular dynamics behavior, energetic properties, vibrational and electronic spectra. We also discussed in depth the electronic structure of N18, including nature of the N-N bonds, lone-pairs, charge distribution characteristics, electronic delocalization, and aromaticity. This work is not only the first exploration of the macrocyclic N18 molecule, but also the first time to systematically examine a very long-chain substance fully composed of nitrogen atoms in isolated state.

Electronic analysis of n-propyl xanthate complexes with group 12 metals: a theoretical-experimental study.

Xanthates are organic compounds of great interest in coordination chemistry due to their different basic sites, which allow them to form complexes with different coordination modes and geometries. These compounds are relevant in the environment and act as heavy metal collectors in aqueous environments. In this theoretical-experimental work, electronic spectroscopy studies of n-propyl xanthate complexes with group 12 metals were performed. This study verified structural differences in these systems, depending on the environment in which they are inserted. In addition, structural differences were observed when the solid was changed to an n-hexane solution. Thus, it was observed that the complexes assume a mononuclear structure in solution, while they present a polymeric form in the solid phase. The electronic spectra obtained through TD-DFT calculations were compared to those of the previously synthesized complexes. In the final theoretical analysis, the main orbitals involved in these transitions were assigned using population analysis calculations. The synthesis of the complexes was confirmed through infrared (MID and FAR), UV‒Vis, Raman, and NMR-1H spectroscopic analyses. The structures of the mononuclear and polymeric complexes were optimized in vacuum and n-hexane. Under vacuum, DFT levels M06L/6-311 + + G** + LANL2TZ and M06L/def2-TZVP were used for the mononuclear complexes, and M06L/LANL2DZ + LANL2 were used for the polymer complexes. For the calculations of the mononuclear complexes in n-hexane, the same level of theory was used for the solid state. TD-DFT calculations for 300 excited states were performed with the same levels of theory and used the optimized structures of the complexes. Furthermore, population analysis was carried out on all the systems studied. Gaussian 09 software was used for the structure optimization, TD-DFT, and population analysis calculations. GaussSum software was used to evaluate the molecular orbitals and electronic spectra.

Geometry optimization and UV/Vis spectra of organometallic chalcones functionalized with a benzo‐15‐crown‐5 fragment: A DFT/TD-DFT investigation

In this paper, we studied the structural and UV–visible absorption spectrum of the organometallic chalcones from ferrocene and cyrhetrene functionalized with a benzo‐15‐crown‐5 fragment. The influence of different alkali and alkaline earth metal ions on geometric structures, frontier molecular orbitals character, gap energy and electronic absorption spectra of [(η5-C5H4C(O)CH = CH-4-benzo-15-crown5)MLn] (MLn = Fe(η5-C5H5) and Re(CO)3) has been theoretically studied by density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations with PBE0 and CAM-B3LYP hybrid functionals. Calculated geometric parameters of studied complexes are in good agreement with the available experimental values. The theoretical absorption spectra reproduce the main properties of the experimental spectra. Both alkali (Li+, Na+, K+, Rb+ and Cs+) and alkaline-earth (Be2+, Mg2+ and Ca2+) metal ions selective complexes have been theoretically identified. The calculated values the lowest energy band (λmax) of the crown ether derivatives to the alkaline earth metal cations increases from Be, Mg, and then Ca in the complexes [2 M], indicating that these absorption bands are associated to a transition from the HOMO to LUMO transition, which is assigned to metal-to-ligand charge transfer (MLCT).

Highlighting non-covalent interactions to molecular structure, electronic and vibrational spectra in a new hybrid organic-inorganic cobalt complex: synthesis, experimental and computational study

Abstract In this study, a novel hybrid organic-inorganic compound, 4-(ammoniummethyl)pyridinium tetracholoraobaltate(II) monohydrate, with non-centrosymmetric properties have been synthesized and characterized by several techniques of powder and single-crystal X-ray diffraction, infrared IR and UV–Visible spectroscopies, and calorimetric (DSC) and the thermogravimetric (TG) analysis. The crystallization of this hybrid compound was found in a monoclinic system with a P21 space group. Additionally, the optimized structures of cation, anion and compound by using hybrid B3LYP method with 6-311++G(d,p) and 6-31+G(d) basis sets shown good correlations with the experimental data and the complete vibrational assignments and force constants are reported for three species. The surface morphology and the micrographs were checked by the scanning electron microscopy (SEM). The UV–Visible absorption spectrum has been used to study the optical properties and the energy gap of our compound. Hirshfeld surface (HS) analysis associated matched up with 2D fingerprint plots were used to confirm the existence of intermolecular and non-covalent interactions in the compound and confirmed by several topological approaches: Quantum Theory of Atom-in-Molecules (QTAIM), reduced density gradient (RDG) and molecular electrostatic potential surface (MEP). The frontier molecular orbitals HOMO and LUMO have been investigated for chemical reactivity and kinetic stability.

New aromatic hydrazones: Synthesis, structural analysis, DFT study, biological activity, ADME-T properties and in silico evaluation of their inhibition of SAS-CoV-2 main protease

Three new hydrazones namely: (2E)-1-(4-methylphenyl-2-[(thiophen-2-yl)methylidene]hydrazine (HZ-1), (2E)-1-(4-methylphenyl)-2-[(thiophen-3yl)methylidene]hydrazine (HZ-2) and (1E)-1[(furan-2-yl)methylidene]-2-(4methylphenyl)hydrazine (HZ-3) have been synthesized by reacting (4-methylphenyl)hydrazine with three heterocyclic aldehydes: 2-thiophenecarboxaldehyde, 3-thiophenecarboxaldehyde and 2-furaldehyde in ethanol at reflux 78 °C. The structures of these compounds were confirmed by spectroscopic and physicochemical methods such as UV–Vis, IR, melting point, 1H NMR and 13C NMR spectra. Their antioxidant activity was evaluated using DPPH, ABTS, FRAP, CUPRAC and phenanthroline assays. The obtained results indicate that the title molecules exhibit excellent activity better and comparable as standards BHT, BHA and ascorbic acid. Also, the synthesized compounds show a good antibacterial activity against two such: P. aeruginosa and B. subtilis. In addition, the density functional theory (DFT) is used to calculate the optimized molecular structures, electronic and vibrational spectra, reactivity, stability and some quantum chemical parameters of the synthesized molecules. The obtained theoretical results are in good agreement with the experimental results. Finally, in silico predictions of ADME-T and pharmacokinetic parameters indicated that these compounds should have good oral bioavailability. Also, the molecular docking has been used to predict the inhibitory activity of SARS-CoV-2 main protease (Mpro) of the studied hydrazones.

Franck-Condon spectra of unbound and imaginary-frequency vibrations via correlation functions: A branch-cut free, numerically stable derivation.

Molecular electronic spectra can be represented in the time domain as auto-correlation functions of the initial vibrational wavepacket. We present a derivation of the harmonic vibrational auto-correlation function that is valid for both real and imaginary harmonic frequencies. The derivation rests on Lie algebra techniques that map otherwise complicated exponential operator arithmetic to simpler matrix formulas. The expressions for the zero- and finite-temperature harmonic auto-correlation functions have been carefully structured both to be free of branch-cut discontinuities and to remain numerically stable with finite-precision arithmetic. Simple extensions correct the harmonic Franck-Condon approximation for the lowest-order anharmonic and Herzberg-Teller effects. Quantitative simulations are shown for several examples, including the electronic absorption spectra of F2, HOCl, CH2NH, and NO2.

Synthesis, characterization, theoretical calculations of novel benzoic acid based azo molecules and their use in effective extraction of Hg(II) ions from aqueous medium

In this study, two series of benzoic acid derivative azo compounds were synthesized using coupling reaction and characterized by various spectroscopic techniques. By using o-, m-, p-chloroaniline and o-, m-, p-nitroaniline as starting materials, the effects of the directing groups on the color intensity of azo dyes were investigated. It was concluded that the nitro group increased both the reaction efficiency and the color intensity. Optimized molecular structures, vibrational and electronic transition spectra, NMR chemical shift values, frontier molecular orbitals and MEP diagrams of each molecule were calculated using the 6-311G(d,p) basis set. All calculations were performed and compared with both Density Functional Theory (DFT) and Hartree-Fock (HF) methods. Experimental and theoretical results were found to be quite compatible with each other. The extraction capabilities of all synthesized azo derivatives were investigated using various transition metal picrates such as Mn2+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+, Hg2+, Pb2+ cations. Solvent extraction studies of azo derivatives revealed that all compounds showed strong binding ability against Cu2+ and especially Hg2+ ions and were able to remove the Hg2+ cation from aqueous medium at a high rate (97.3%).

Theoretical study on the optical properties of an ESIPT-based fluorescent probe for phosgene.

A fluorescent probe Pi with the excited-state intramolecular proton transfer (ESIPT) properties was synthesized and used to detect the phosgene in solution and gas phases. However, the detection mechanism of the fluorescent probe needs to be further studied. Herein, the density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods were adopted to explore the molecular structures and electronic spectra properties of probe and its product Pio after reacting with phosgene. Through analysis for molecular structure parameters and infrared vibrations accompanied with the hydrogen bond of Pi, it is confirmed that the intramolecular hydrogen bond of Pi is enhanced under light excitation, which illustrates the occurrence of ESIPT reaction combined with the scanned potential energy curves. It can be seen from the simulated spectra that Pi shows double fluorescence through ESIPT process, while the fluorescent product Pio exhibits the single fluorescence due to the disappearance of intramolecular hydrogen bond. Through the study on the structure and optical properties of Pi and Pio, it can be helpful to deeply understand the intrinsic mechanism of the detection of phosgene by the Pi molecule probe, which also supplies a reference to the further study about the fluorescence probe.

Targeted synthesis of two iron(III) tetradentate dibasic chelating Schiff base complexes toward inhibition of acidic induced steel corrosion: Empirical and DFT insights

Two new azomethine chelates for Fe3+ ions were prepared from two dibasic tetradentate chelating imine ligands. The studied Schiff base ligands were 2,2′‐((1E,1′E)‐((4‐nitro‐1,2‐phenylene)bis(azanylylidene))bis(methanylylidene))bis(4‐bromophenol) (NABS) and 2,2′‐((1E,1′E)‐((4,5‐dimethyl‐1,2‐phenylene)bis(azanylylidene))bis(methanylylidene))bis(4‐bromophenol) (MABS). Alternative spectral and physicochemical tools such as Fourier transform infrared spectroscopy (FTIR), C13 NMR, 1H NMR, and CHN analyses, thermogravimetric analysis (TGA), molecular electronic spectra, and magnetic susceptibility measurements were applied to inspect the structural composition of the compounds under investigation. In addition, the DFT approach was used to optimize the geometry of all compounds in order to get ideal structures and important characteristics. The synthesized compounds examined as an anticorrosive films of C‐steel in acidic chloride medium utilizing theoretical and electrochemical studies such electrochemical impedance spectroscopy (EIS), potentiodynamic polarization (PDP), and potentiodynamic anodic polarization curve (PAP) approaches. The inhibition efficiency augmented with the increasing of the inhibitor dose. The prepared Schiff bases and their iron complexes exhibited protection capacity around 96.8% in the presence of 0.5 mmol L−1. PDP outcomes approve the additive molecules act as mixed inhibitors. The Langmuir model is followed by Schiff bases and their iron complexes as it is contains both chemical and physical adsorption on the metal interface. The surface morphology of the substrate (in blank and inhibited systems) was scanned using field‐emission scanning electron microscopy (FESEM). A good agreement among experimental techniques and corresponding density functional theory (DFT) results was found, which confirmed the purity of the studied compounds and suggested octahedral geometry around Fe(III) ions in both MABSFe and NABSFe complexes.

Reconstruction of Nuclear Ensemble Approach Electronic Spectra Using Probabilistic Machine Learning.

The theoretical prediction of molecular electronic spectra by means of quantum mechanical (QM) computations is fundamental to gain a deep insight into many photophysical and photochemical processes. A computational strategy that is attracting significant attention is the so-called Nuclear Ensemble Approach (NEA), that relies on generating a representative ensemble of nuclear geometries around the equilibrium structure and computing the vertical excitation energies (ΔE) and oscillator strengths (f) and phenomenologically broadening each transition with a line-shaped function with empirical full-width δ. Frequently, the choice of δ is carried out by visually finding the trade-off between artificial vibronic features (small δ) and over-smoothing of electronic signatures (large δ). Nevertheless, this approach is not satisfactory, as it relies on a subjective perception and may lead to spectral inaccuracies overall when the number of sampled configurations is limited due to an excessive computational burden (high-level QM methods, complex systems, solvent effects, etc.). In this work, we have developed and tested a new approach to reconstruct NEA spectra, dubbed GMM-NEA, based on the use of Gaussian Mixture Models (GMMs), a probabilistic machine learning algorithm, that circumvents the phenomenological broadening assumption and, in turn, the use of δ altogether. We show that GMM-NEA systematically outperforms other data-driven models to automatically select δ overall for small datasets. In addition, we report the use of an algorithm to detect anomalous QM computations (outliers) that can affect the overall shape and uncertainty of the NEA spectra. Finally, we apply GMM-NEA to predict the photolysis rate for HgBrOOH, a compound involved in Earth’s atmospheric chemistry.

Theoretical prediction of pH-dependent electronic spectra in aqueous solution: A combinational application of QM/MM calculations and constant-pH simulations with configuration-selection scheme

We propose a self-contained theoretical methodology to predict the pH effects on the molecular electronic spectra in aqueous solution, combining our recently developed the configuration-selection (CS) constant-pH (CpH) simulation (CS-CpH) method with quantum mechanics/molecular mechanics (QM/MM) method. By computationally sampling many protonation state transitions by CS-CpH simulations and estimating the electronic energies by QM/MM calculations, we can obtain the theoretical description of the pH dependent electronic spectra. As an example, we applied the present methodology to para-nitrophenol (pNP) in aqueous solution, and demonstrated that the method could successfully reproduce the electronic transition energies and the isosbestic point.

Spectroscopic (FTIR, UV-Vis, NMR) investigations, DFT predictions of global reactivity descriptors and efficient corrosion inhibitors of N-carbobenzoxy-L-ValineSuccinimidyl Ester

The stable conformation of molecular structure, vibrational frequencies and electronic absorption spectra of N-Carbobenzoxy-L-Valine-Succinimidyl Ester were established using DFT/B3LYP/6-311G basis set calculations. The compound was characterized by spectroscopic profiling employing FT-IR, UV–Visible and NMR spectra both experimentally and theoretically. The HOMO–LUMO analysis was carried out with different applied electric fields. Molecular Electrostatic Potential (MEP), First order hyperpolarizability, and Fukui functions calculation were also performed. The global reactivity descriptors were calculated to establish the relationship between the descriptors and corrosion inhibition efficiency. Molecular orbital calculations reveal that the molecule may be bioactive based on its global reactivity.

Computational molecular design of NIR dyes with varying anchoring groups for improving the efficiency and stability of dye-sensitized solar cells

Design and development of near-infrared (NIR) dyes with strong binding on the TiO2 surface is inevitable for the realization of the dye-sensitized solar cells (DSSCs) with improved efficiency and stability. A series of NIR dyes bearing different anchoring groups have been designed considering their suitability as sensitizers for DSSCs based-on TiO2 and iodine-based redox electrolytes. Under the Gaussian program, density functional theory (DFT)/6-311G/B3PW91 level of theory and time-dependent-DFT using the polarizable continuum model is shown optimum for the prediction of the highest occupied molecular orbital energy level and electronic absorption spectra. The reliability of the calculated results was validated by corresponding experimental results for some of the representative dyes. It has been demonstrated that λ max at full width at half maximum in calculated absorption spectra exhibited an excellent match with the experimentally estimated Eg of the sensitizers leading to the proposal of a new method for the construction of the theoretical energy band diagram. Amongst newly designed sensitizers, dyes bearing dual anchoring groups like SQ-149, SQ-150, SQ-158, SQ-161 and SQ-162 are highly promising not only for good NIR photon harvesting but also to impart to improved DSSC stability.

Calculating Multidimensional Optical Spectra from Classical Trajectories

Multidimensional optical spectra are measured from the response of a material system to a sequence of laser pulses and have the capacity to elucidate specific molecular interactions and dynamics whose influences are absent or obscured in a conventional linear absorption spectrum. Interpretation of complex spectra is supported by theoretical modeling of the spectroscopic observable, requiring implementation of quantum dynamics for coupled electrons and nuclei. Performing numerically correct quantum dynamics in this context may pose computational challenges, particularly in the condensed phase. Semiclassical methods based on calculating classical trajectories offer a practical alternative. Here I review the recent application of some semiclassical, trajectory-based methods to nonlinear molecular vibrational and electronic spectra.

Comment on "Theoretical investigation on bond and spectrum of cyclo[18]carbon (C18) with sp-hybridized".

Recently, Shuhong Xu et al. reported theoretical calculation of molecular structure, bonding, aromaticity, electron delocalization, and electronic spectrum of cyclo[18]carbon in J. Mol. Model., 26, 111 (2020). Due to inappropriate consideration of calculation strategy, misunderstanding of some analysis methods and concepts, and some errors in the data, there are misleading statements and unconvincing conclusions in their paper. Here, we will point out inadequacies of Shuhong Xu's paper and put forward our own views. The contents of this comment will also help those who are studying cyclo[18]carbon to better understand this system and its analogues.

Computational study of IR, Raman, and NMR spectra of 4-methylmethcathinone drug.

Molecular electronic structure, IR, UV, and NMR spectra of the most popular cathinone, known as mephedrone or 4-methylmethcathinone (4-MMC), is studied thoroughly by quantum chemical calculation in terms of the density functional theory (DFT). Geometry optimization of 4-MMC and its hydrochloride complex is performed with the B3LYP functional, and all vibrational frequencies are analyzed in all details. On this background, the IR and Raman spectra are interpreted. The importance of low-frequency terahertz and Raman spectra is stressed for distinguishing of various MMC isomers. The UV spectrum is calculated by time-dependent DFT method which allows complete interpretation of intense absorption bands at 270 and 210nm as combinations of various ππ*, nπ*, and charge transfer excitations in amino-phenyl moieties. Very informative analysis of UV absorption and NMR spectra provides useful details on the structure-activity relationship for mephedrone molecule.

Experimental and first-principles study of a new hydrazine derivative for DSSC applications

Hydrazine derivatives have a wide variety of applications in organic synthesis, material science, medical treatments, as well as the dye-sensitized solar cells (DSSC). In this work, the molecular structure, electronic spectra and first principles investigation for the exo-endo isomerization in (1E,2E)-bis[1-(4-nitrophenyl)ethylidene]hydrazine were studied. The structural interactions and synthon formations have been determined experimentally via Hirshfeld surface analysis (HSA) and two-dimensional fingerprint plots (2D-FP). Furthermore, the solid-state XRD/HSA interactions have been used to explain the physical behavior of the compound. The transition state for the exo-endo isomerization was located using density functional theory (DFT). The activation barrier is estimated to be 110.5 kJ/mol (in vacuo). The endo isomer was found to be slightly more stable than the exo one. The UV-Vis spectra of the two isomers were obtained using time-dependent density functional theory (TDDFT) and compared to the experimental spectra in vacuo, water, and methanol. To explore the potential of the new compound as a DSSC sensitizer, the emission spectrum was also constructed by optimizing the singlet electronic excited state.

Theoretical investigation on the ESIPT mechanism and fluorescent sensing mechanism of 2-(2′-hydroxyphenyl) thiazole-4-carboxaldeyde in methanol

2-(2'-Hydroxyphenyl) thiazole-4-carboxaldeyde (aldehyde 1) and hemiacetal 2 were selected to study the mechanism of excited-state intramolecular proton transfer and the detecting of Al3+ ion in methanol by using density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods. Our theoretical results are in good agreement with the experimental values. The intramolecular H-bond is enhanced in the first excited-state based on the analyses of structural parameters, frontier molecular orbitals and electronic spectra. The stronger intramolecular H-bond is more favorable for ESIPT process. In order to further demonstrate the proton transfer process, we constructed the potential energy curves of probe 1 and 2 in both ground- and excited-states, and concluded that proton transfer processes in probe 1 and 2 are apt to happen in the S1 state. In addition, the Mayer bond order, energy gap and absorption and fluorescence spectra were applied to interpret the process of detection of Al3+ ion.

Spectroscopic and DFT studies, structural determination, chemical properties and molecular docking of 1-(3-bromo-2-thienyl)-3-[4-(dimethylamino)-phenyl]prop-2-en-1-one

The bromo based theyophen chalcone derivative 1-(3-Bromo-2-thienyl)-3-[4-(dimethylamino)-phenyl] prop-2-en-1-one (BTDAP) has been investigated by spectroscopy and quantum chemistry methods using Gaussian09 software package. The stable conformation of molecular structure, vibrational frequencies and electronic absorption spectra were established using B3LYP/6-311++G(d,p) and M062x/6-311++G(d,p) calculations. The Infrared intensities, Raman scattering active regions have been calculated. UV–Visible absorption spectrum has showed the best agreement with their experimental results. The formation of the donor and the acceptor stabilization energies, molecular bonding which is composed from orbitals that have been localized on different atoms and molecular bond angular properties were investigated using NBO, NLMO and NHO calculations. Frontier molecular orbital analysis which explains the energy gap between the ground state HOMO and first excited state LUMO energies were determined. Besides, the chemical properties of condensed Fukui function, MEP and electron-hole charge transfer within the molecule due to excitation for three excited states were obtained by multiwfn software. Molecular docking studies were performed for the title compound with Monoamine oxidase A and B inhibitions.

Spectroscopic and structural investigations on modafinil by FT-IR, FT-Raman, NMR, UV-Vis and DFT methods.

Chiral sulfoxide based smart drug modafinil were studied experimentally and theoretically. Vibrational spectra were recorded in the mid IR region and electronic spectra were recorded in UV-Visible region. The molecular geometry, vibrational spectra, magnetic spectra and electronic spectra were simulated using Density Functional Theory (DFT) employed with B3LYP/6-311++G(d,p) basis set. The molecular geometry optimization, vibrational frequencies, chemical shifts and solvent effect on electronic properties were reported. The intermolecular interactions have been studied by Hirshfeld surface analysis. There is good agreement was found between calculated and observed values, thereby to confirm the molecular structure of modafinil.