Quantum Chemical Study Research Articles

Can Coordinated Water be a Good Hydrogen Bond Acceptor? Crystallographic and Quantum Chemical Study

Can Coordinated Water be a Good Hydrogen Bond Acceptor? Crystallographic and Quantum Chemical Study

A Study Modeling Bridged Nucleic Acid-Based ASOs and Their Impact on the Structure and Stability of ASO/RNA Duplexes.

Antisense medications treat diseases that cannot be treated using traditional pharmacological technologies. Nucleotide monomers of bare and phosphorothioate (PS)-modified LNA, N-MeO-amino-BNA, 2',4'-BNANC[NH], 2',4'-BNANC[NMe], and N-Me-aminooxy-BNA antisense modifications were considered for a detailed DFT-based quantum chemical study to estimate their molecular-level structural and electronic properties. Oligomer hybrid duplex stability is described by performing an elaborate MD simulation study by incorporating the PS-LNA and PS-BNA antisense modifications onto 14-mer ASO/RNA hybrid gapmer type duplexes targeting protein PTEN mRNA nucleic acid sequence (5'-CTTAGCACTGGCCT-3'/3'-GAAUCGUGACCGGA-5'). Replica sets of MD simulations were performed accounting to two data sets, each set simulated for 1 μs simulation time. Bulk properties of oligomers are regulated by the chemical properties of their monomers. As such, the primary goal of this work focused on establishing an organized connection between the monomeric BNA nucleotide's electronic effects observed in DFT studies and the macroscopic behavior of the BNA antisense oligomers, as observed in MD simulations. The results from this study predicted that spatial orientation of MO-isosurfaces of the BNA nucleotides are concentrated in the nucleobase region. These BNA nucleotides may become less accessible for various electronic interactions when coupled as ASOs forming duplexes with target RNAs and when the ASO/RNA duplexes further bind with the RNase H. Understanding such electronic interactions is crucial to design superior antisense modifications with specific electronic properties. Also, for the particular nucleic acid sequence solvation of the duplexes although were higher compared to the natural oligonucleotides, their binding energies being relatively lower may lead to decreased antisense activity compared to existing analogs such as the LNAs and MOEs. Fine tuning these BNAs to obtain superior binding affinity is thus a necessity.

Synthesis, Crystal Structure and Antifungal Activity of (E)-1-(4-Methylbenzylidene)-4-(3-Isopropylphenyl) Thiosemicarbazone: Quantum Chemical and Experimental Studies.

A novel (E)-1-(4-methylbenzylidene)-4-(3-isopropylphenyl) thiosemicarbazone was synthesized in a one-pot four-step synthetic route. Fourier transform infrared spectroscopy (FTIR), 1H and 13C nuclear magnetic resonances (NMR), single-crystal X-ray diffraction, and UV-visible absorption spectroscopy were utilized to confirm the successful preparation of the title compound. Single-crystal data indicated that the intramolecular hydrogen bond N(3)-H(3)···N(1) and intermolecular hydrogen bond N(2)-H(2)···S(1) (1 - x, 1 - y, 1 - z) existed in the crystal structure and packing of the title compound. Besides the covalent interaction, the non-covalent weak intramolecular hydrogen bond N(3)-H(3)···N(1) discussed by atoms in molecules (AIM) theory also functioned in maintaining the title compound's crystal structure. The strong intermolecular hydrogen bond N(2)-H(2)···S(1) (1 - x, 1 - y, 1 - z) discussed by Hirshfeld surface analysis played a major role in maintaining the title compound's crystal packing. The local maximum and minimum electrostatic potential of the title compound was predicted by electrostatic potential (ESP) analysis. The UV-visible spectra and HOMO-LUMO analysis revealed that the title compound has a low ΔEHOMO-LUMO energy gap (3.86 eV), which implied its high chemical reactivity due to the easy occurrence of charge transfer interactions within the molecule. Molecular docking and in vitro antifungal assays evidenced that its antifungal activity is comparable to the reported pyrimethanil, indicating its usage as a potential candidate for future antifungal drugs.

A Framework for Incorporating Binding Energy Distribution in Gas-ice Astrochemical Models

Abstract One of the most serious limitations of current astrochemical models with the rate equation (RE) approach is that only a single type of binding site is considered in grain surface chemistry, although laboratory and quantum chemical studies have found that surfaces contain various binding sites with different potential energy depths. When various sites exist, adsorbed species can be trapped in deep potential sites, increasing the resident time on the surface. On the other hand, adsorbed species can be populated in shallow sites, activating thermal hopping and thus two-body reactions even at low temperatures, where the thermal hopping from deeper sites is not activated. Such behavior cannot be described by the conventional RE approach. In this work, I present a framework for incorporating various binding sites (i.e., binding energy distribution) in gas-ice astrochemical models as an extension of the conventional RE approach. I propose a simple method to estimate the probability density function (pdf) for the occupation of various sites by adsorbed species, assuming a quasi-steady state. By using thermal desorption and hopping rates weighted by the pdfs, the effect of binding energy distribution is incorporated into the RE approach without increasing the number of ordinary differential equations to be solved. This method is found to be accurate and computationally efficient, and enables us to consider binding energy distribution even for a large gas-ice chemical network which contains hundreds of icy species. The impact of the binding energy distribution on interstellar ice composition is discussed quantitatively for the first time.

Quantum-chemical study of alkyl- and alkenyladamantanes formation by ionic alkylation with olefins

In B3LYP-D3(BJ)/6-311++G** approximation thermodynamic parameters of formation reactions (total energy at 0 К, enthalpy and the Gibbs free energy at temperature 298.15 К and pressure 101325 Pa) are assessed for the products of ionic alkylation of adamantane and lower alkyladamantanes with ethylene and propylene. Aluminium chloride was used as acid catalyst model. Quantum-chemical calculations demonstrate the influence of methyl groups in adamantanes and olefin molecular weight on energetics of formation of relevant alkyl- and alkenyladamantanes.

Experimental, quantum chemical spectroscopic investigation, topological, molecular docking/dynamics and biological assessment studies of 2,6-Dihydroxy-4-methyl quinoline

The present work is a comprehensive investigation of the spectral, electronic structure, bonding, and reactivity of the 2,6-dihydroxy-4-methylquinoline (26DH4MQ) molecule through a wide range of experimental and quantum chemical spectroscopic calculations techniques, along with its applications as nonlinear optical materials and biological assessments. The study utilized density functional theory (DFT) and time-dependent density functional theory (TD-DFT) with the B3LYP method and the 6-311G++(d,p) basis set to analyze the structural and molecular properties of 26DH4MQ. The findings from UV–Vis, FT-IR, and FT-NMR spectroscopy show a strong agreement between the experimentally obtained vibrational frequencies and chemical shifts and those predicted by computational methods. Local reactivity descriptors, such as the dual descriptor, Fukui functions, and the molecular electrostatic potential (MEP) map, were used to identify the reactive regions of the molecule. Additionally, natural bond orbital (NBO) analysis provided insights into the charge transfer characteristics of 26DH4MQ, which helps to stabilize the molecular system. The study also revealed notable nonlinear optical (NLO) properties, with polarizability (18.52 × 10–24e.s.u.) and first-order hyperpolarizability (2.26 × 10–30e.s.u.) values that surpass those of standard organic compounds, suggesting significant potential for optoelectronic applications. The biological evaluation of 26DH4MQ assessed its drug-likeness, toxicity, enzyme inhibition, and ADME (Absorption, Distribution, Metabolism, and Excretion) parameters, highlighting its pharmaceutical potential. Furthermore, molecular docking and dynamics studies illustrated the compound's interaction with proteins, indicating its potential role as an insulin inhibitor.

Proton Conduction via Water and Ammonia Coordinated Metal Cationic Species in MOF and MHOF Platforms.

Although metal-organic frameworks (MOFs) and metalo hydrogen-bonded organic frameworks (MHOFs) are designed as promising solid-state proton conductors by incorporating various protonic species intrinsically or extrinsically, design and development of such materials by employing the concept of proton conduction through coordinated polar protic solvent is largely unexplored. Herein, we have constructed two proton-conducting materials having different solvent coordinated metal cationic species: In-H2O-MOF, ({[In(H2O)6][In3(Pzdc)6]·15H2O}n; H2Pzdc: pyrazine-2,3-dicarboxylic acid) with coordinated water molecules from hexaaquaindium cationic species, and MHOF-4, ([{Co(NH3)6}2(2,6-NDS)2(H2O)2]n; 2,6-H2NDS: 2,6-naphthalenedisulfonic acid) with coordinated ammonia from hexaammoniacobalt cationic species. Interestingly, higher proton conductivity was achieved for In-H2O-MOF (1.5 × 10-5 S cm-1) than MHOF-4 (6.3 × 10-6 S cm-1) under the extreme conditions (80 ºC and 95% RH), which could be attributed to enhanced acidity of coordinated water molecules having much lower pKa value than that of coordinated ammonia. Greater charge polarization on hydrogen atoms of In3+-coordinated water molecules than that of Co2+-coordinated ammonia led to the high conductivity of In-H2O-MOF, as evident by quantum chemical studies. Such a comparative study on metal-coordinated protic polar solvents in achieving proton conduction in crystalline solids is yet to be made.

Exploring the impact of heterocyclic bridges for tuning the amplitudes of Nonlinear optical properties under Gas, IEFPCM and COSMO solvent models

Nonlinear optical (NLO) materials are a distinctive class of materials due to their NLO response and wide range of applications. We present a systematic quantum chemical study for designing triphenylamine based derivatives (1Ph to 3PhDTDZ) by modifying central bridge with various size and types of heterocyclic rings. Density functional theory (DFT) method is used to calculate the NLO properties including linear and third-order NLO polarizabilities (α and γ) by using M06-2X functional coupled with the 6-311G** basis set. The calculation results predict that among the designed compounds, 1PhDTDZ has the highest third-order NLO polarizability of 2347.7 x 10−36 esu and lowest transition energy of 1.828 eV. On the other hand, 3PhDTDZ has a greater amplitude (108.5 x 10−24 esu) of static linear polarizability (αiso). We also computed frequency-dependent third-order NLO polarizability values at various laser wavelengths (1500 nm to 1970 nm). This provides valuable information about the complex interaction between light and matter. Dynamic second hyperpolarizability of electro-optic Pockels effect (EOPE effect, (γ (−ω; ω,0,0)) is calculated at 1500 nm laser wavelength with a larger γ-amplitude of 36708.4 x 10−36 esu. The effect of solvent on α and γ has also been the primary focus of this research. An extensive solvation impact has been studied using integral equation formalism Polarizable Continuum Model (IEFPCM) and Conductor-like Screening Model (COSMO). Magnitudes of αiso and 〈γ〉 have shown variation from gas to solvent methods. While among solvents, amplitudes are seen 3.87 % to 11.29 % greater under the effect of COSMO-methanol than PCM-methanol. The Frontier molecular orbital (FMO) studies found a significant decrease in energy band gaps from 5.75 eV to 2.98 eV. Since our systems exhibit remarkable photovoltaic properties, they can be used as dye-sensitized solar cells (DSSCs). Their open circuit voltage (VOC) ranging from 1 eV to 4 eV. Thus, our designed triphenylamine based derivatives with distinct central heterocyclic bridges showcase remarkable efficiency as NLO materials, with additional benefits of exhibiting good photovoltaic properties.

Quantum Chemical Study, In Silico ADMET Profile Analysis, Molecular Docking, and MD Simulation of 5-(Furan-2-ylmethylidene) thiazolo[3,4-a] benzimidazole-2-thione

Quantum Chemical Study, In Silico ADMET Profile Analysis, Molecular Docking, and MD Simulation of 5-(Furan-2-ylmethylidene) thiazolo[3,4-a] benzimidazole-2-thione

Extensive reference set and refined computational protocol for calculations of 57Fe Mössbauer parameters.

Mössbauer spectroscopy is a powerful technique for probing the local electronic structure of iron compounds, because it reports in an element-selective manner on both the oxidation state and coordination environment of the Fe ion. Computational prediction of the two main Mössbauer parameters, isomer shift (δ) and quadrupole splitting (ΔEQ), has long been targeted by quantum chemical studies, and useful protocols based on density functional theory have been proposed. Here we present an extensive curated reference set of Fe compounds that is considerably larger and more diverse than literature precedents. We make a distinction between low-temperature and high-temperature experimental subgroups. This set is employed for optimizing a refined computational protocol utilizing the scalar version of the exact 2-component (X2C) Hamiltonian with the finite nucleus approximation. Attention is devoted to having an accurate and flexible all-electron basis set for Fe. We assess the performance of several DFT methods that cover all representative families and rungs of functionals and find that hybrid functionals with ca. 25-30% exact exchange offer the best accuracy for isomer shifts. The work establishes a refined general protocol of wide applicability that achieves good performance for the prediction of isomer shifts in a wider variety of systems than before, but the limitations of DFT for quadrupole splittings are also highlighted. Finally, comparison of calculated values with high-temperature experimental results shows that the use of an empirical correction factor is required to account for the second-order Doppler shift and to achieve the same quality of correlation as with the low-temperature data.

Adducts of bovine serum albumin and binuclear nitrosyl iron complex with thiosulfate ligands: a molecular docking and quantum chemical study

Adducts of bovine serum albumin and binuclear nitrosyl iron complex with thiosulfate ligands: a molecular docking and quantum chemical study

Single Crystal, Spectroscopic Measurement, Quantum Chemical Studies, and Antimicrobial Potency of a new Cadmium Compound as a Potential Candidate for Therapeutic Antibacterial drug Development

Single Crystal, Spectroscopic Measurement, Quantum Chemical Studies, and Antimicrobial Potency of a new Cadmium Compound as a Potential Candidate for Therapeutic Antibacterial drug Development

Effect of electron-donating and -withdrawing substitutions in naphthoquinone sensitizers: The structure engineering of dyes for DSSCs in Quantum Chemical Study

Dye-sensitized solar cells (DSSCs) are cost-effective photovoltaic devices that convert solar energy into electricity using a dye sensitizer, TiO2 photoanode, electrolyte, and counter electrode. This study investigates the impact of substituents on the performance of naphthoquinone-based dye sensitizers in DSSCs. We analyzed various naphthoquinone derivatives’ electronic structures and light absorption properties using DFT and TD-DFT. Our results demonstrate that electron-donating groups enhance DSSC performance by improving light absorption and electron injection. Specifically, naphthoquinone derivatives with methoxy (Dye-2) and methyl (Dye-3) groups showed superior properties. TD-DFT analysis revealed high molar extinction coefficients over a broad spectrum, making these dyes efficient at capturing sunlight. Additionally, these dyes effectively interact with TiO2, which is crucial for photostability and photovoltaic performance. In conclusion, naphthoquinone derivatives with electron-donating groups significantly improve DSSC performance, with Dye-2 and Dye-3 being strong candidates for high-performance applications.

Synthesis, photophysical characterisation, quantum-chemical study and in vitro antiproliferative activity of cyclometalated Ir(III) complexes based on 3,5-dimethyl-1-phenyl-1H-pyrazole and N,N-donor ligands.

In this paper, we present the synthesis of four new complexes: the dimeric precursor [Ir(dmppz)2(μ-Cl)]2 (1) (Hdmppz - 3,5-dimethyl-1-phenyl-1H-pyrazole) and heteroleptic bis-cyclometalated complexes: [Ir(dmppz)2(Py2CO)]PF6·½CH2Cl2 (2), [Ir(dmppz)2(H2biim)]PF6·H2O (3), and [Ir(dmppz)2(PyBIm)]PF6 (4), with auxiliary N,N-donor ligands: 2-di(pyridyl)ketone (Py2CO), 2,2'-biimidazole (H2biim) and 2-(2'-pyridyl)benzimidazole (PyBIm). In the obtained complexes, SC-X-ray analysis revealed that Ir(III) has an octahedral coordination sphere with chromophores of the type {IrN2C2Cl2} (1) or {IrN4C2} (2-4). The complexes obtained, which have been fully characterised by physicochemical methods (CHN, TG, FTIR, UV-Vis, PL and 1H, 13C, 15N NMR), were used to continue our studies on the factors influencing the cytotoxic properties of potential chemotherapeutic agents (in vitro). To this end, the following studies are presented: (i) comparative analysis of the effects on the biological properties of N,N-donor ligands and C,N-donor ligands in the studied complexes, (ii) studies of the interactions of the compounds with the selected molecular target: DNA and BSA (UV-Vis, CD and PL methods), (iii) and the reactivity towards redox molecules: GSH, NADH (UV-Vis and/or ESI-MS methods), (iv) cytotoxic activity (IC50) of potential chemotherapeutics against MCF-7, K-562 and CCRF-CEM cell lines.

A Theoretical Exploration of the Photoinduced Breaking Mechanism of the Glycosidic Bond in Thymine Nucleotide.

DNA glycosidic bond cleavage may induce cancer under the ultraviolet (UV) effect. Yet, the mechanism of glycosidic bond cleavage remains unclear and requires more detailed clarification. Herein, quantum chemical studies on its photoinduced mechanism are performed using a 5'-thymidine monophosphate (5'-dTMPH) model. In this study, four possible paths were examined to study the glycosidic bond cleavage. The results showed that, upon excitation, the electronic transition from the π bonding to π antibonding orbitals of the thymine ring leads to the damage of the thymine ring. Afterwards, the glycosidic bond is cleaved. At first, the doublet ground state (GS) path of glycosidic bond cleavage widely studied by other groups is caused by free electron generated by photoirradiation, with a kinetically feasible energy barrier of ~23 kcal/mol. Additionally, then, the other three paths were proposed that also might cause the glycosidic bond cleavage. The first one is the doublet excited state (ES) path, triggered by free electron along with UV excitation, which can result in a very-high-energy barrier ~49 kcal/mol that is kinetically unfavorable. The second one is the singlet ES path, induced by direct UV excitation, which assumes DNA is directly excited by UV light, which features a very low-energy barrier ~16 kcal/mol that is favored in kinetics. The third one is the triplet ES path, from the singlet state via intersystem crossing (ISC), which refers to a feasible ~27 kcal/mol energy barrier. This study emphasizes the pivotal role of the DNA glycosidic bond cleavage by our proposed direct UV excitation (especially singlet ES path) in addition to the authorized indirect free-electron-induced path, which should provide essential insights to future mechanistic comprehension and novel anti-cancer drug design.

Difenoconazole solubility in acetonitrile/N,N-dimethylformamide/acetone + water and quantum chemistry study into inter/intra-molecular interactions

The difenoconazole solubilities in acetonitrile/acetone/N,N-dimethylformamide (DMF) + water systems were acquired experimentally with the help of the isothermal shake-flask technique. Analysis of X-ray power diffraction revealed that difenoconazole did not exhibit any crystal transition as well as solvate formation. The solubility acquired here was accurately correlated, which yielded relative average deviations (RAD) of ≤4.99 % and a root-mean-square deviation of ≤20.59 × 10−5 through the Jouyban-Acree and modified van’t Hoff-Jouyban-Acree models Additionally, to explain the solubility behavior at a temperature of 298.15 K, this work examines the acetonitrile/acetone/DMF + water and the previously published methanol/ethanol/isopropanol/PG + water blends utilizing the extended Hildebrand solubility technique. The RAD levels remained below 6.88 %. The dipolarity-polarizability and the solubility parameter of blended solvents exert a substantial impact on the variability of difenoconazole solubility. The preferred solvation of difenoconazole at a temperature of 298.15 K was examined through the inverse Kirkwood-Buff integrals. The solvation parameters’ values of difenoconazole were positive in blends containing methanol, acetone, DMF, ethanol, isopropanol, and acetonitrile with moderate and rich compositions. This indicates that difenoconazole is preferentially solvated by them in above composition ranges. A shift from an enthalpy-driven mechanism to an entropy-driven one was revealed through an analysis of the thermodynamics of the entropy-enthalpy relationship in the dissolution of difenoconazole in blends. Furthermore, the mean local ionization energy, Hirshfeld surface as well as molecular surface electrostatic potential were employed to illustrate the microscopic electrostatic characteristics. The N and N groups in the five-membered ring of difenoconazole molecule are the primary sites for electrophilic attack. The weak contacts of difenoconazole-solvent were demonstrated with the help of a Hirshfeld partition analysis-based independent gradient model.

Biocatalytic Carbenoid N-H Insertions Via Engineered Myoglobins: A Systematic Reaction Mechanism Study

Recently engineered myoglobins have demonstrated excellent biocatalytic activities for a broad range of carbenoid N-H insertion reactions with up to >99% yield. Such biocatalysts offer various tuning points beyond protein residues, such as metal center, and axial ligand, to regulate different chemical reactivities. However, there is no computational mechanistic study to reveal its basic reaction mechanism, which could be utilized to study effects of different catalyst component for rational biocatalyst design. The reported computational mechanistic papers of other heme protein catalyzed N-H insertion have limited information without a careful comparison of all possible pathways and just focused on certain steps. Building on our group’s recent mechanistic work on a number of heme carbene transfer reactions, we performed a quantum chemical study to systematically study all possible reaction pathways for myoglobin catalyzed N-H insertions, which starts from the reactants to final released products and thus constitute a complete reaction pathway study. We examined ylide (proton transfer), hydrogen atom transfer, and hydride transfer pathways. In the favored ylide pathways, we calculated the direct proton transfer from amine to carbene and indirect paths with both concerted and stepwise proton transfer and dissociation components. For the indirect pathways in which the proton resides on the carbonyl oxygen of the original carbene substituent, subsequent water-assisted proton transfer from this carbonyl oxygen to carbene’s carbon to form the final product was also investigated. The most favorable pathway from this systematic reaction mechanism study was further supported by new experimental work from our collaborators, the original developer of myoglobin-based biocatalysts. These novel mechanistic results provide important mechanistic information for future biocatalyst design with enhanced reactivities.

Environment-dependent chlorophyll-chlorophyll charge transfer states in Lhca4 pigment-protein complex.

Photosystem I (PSI) light-harvesting antenna complexes LHCI contain spectral forms that absorb and emit photons of lower energy than that of its primary electron donor, P700. The most red-shifted fluorescence is associated with the Lhca4 complex. It has been suggested that this red emission is related to the inter-chlorophyll charge transfer (CT) states. In this work we present a systematic quantum-chemical study of the CT states in Lhca4, accounting for the influence of the protein environment by estimating the electrostatic interactions. We show that significant energy shifts result from these interactions and propose that the emission of the Lhca4 complex is related not only to the previously proposed a603+-a608- state, but also to the a602+-a603- state. We also investigate how different protonation patterns of protein amino acids affect the energetics of the CT states.

Hydrazine complexes with formic acid formed in the N2H4—HCOOH—HCOO− system in the presence of KOBut—DMSO superbase: a quantum chemical study

Hydrazine complexes with formic acid formed in the N2H4—HCOOH—HCOO− system in the presence of KOBut—DMSO superbase: a quantum chemical study

Pyridyl-Substituted Nitronyl Nitroxides: Comprehensive Magnetochemical and Quantum Chemical Study.

A series of pyridyl-substituted nitronyl nitroxides was synthesized and structurally characterized. A comprehensive magnetochemical and quantum chemical study of extended raw of the nitroxides with different substituents R in the pyridine fragment was performed. It was shown, that temperature-dependent magnetic properties are determined by the short contacts between nitroxide groups of adjacent molecules as well as between nitroxide group and methyl substituents in the pseudo axial positions of imidazoline fragments. Quantum chemistry allows to select the appropriate model of exchange cluster for analysis of experimental magnetic data and evaluation of the exchange interaction parameters. For NN-PyCl the "order-disorder" transition was detected by means of low temperature XRD. The difference in the experimental and calculated exchange interaction energies may serve as an indicator of temperature-induced structural rearrangements. For instance, for methyl substituted nitronyl nitroxide NN-PyMe structural transformations and significant changes in exchange interaction energies were observed.