Bond Parameters Research Articles

Exploring quantum computational, molecular docking, and molecular dynamics simulation with MMGBSA studies of ethyl-2-amino-4-methyl thiophene-3-carboxylate

2-aminothiophenes derivative, Ethyl-2-amino-4-methyl thiophene-3-carboxylate (EAMC) has been synthesized, characterized, and investigated quantum chemically. It was experimentally investigated by different spectroscopic methods like- NMR (1H-NMR and 13C-NMR), FT-IR, and UV-Visible. B3LYP method and 6-311++G(d,p) basis set were employed for optimization of molecular structure and calculation of wave numbers of normal modes of vibrations and various other important parameters. Calculated bond lengths and angles were compared with the experimental bond lengths and Bond Angle Parameters. Optimized bond parameters and experimental bond parameters were found in good agreement. Complete potential energy distribution assignments were done successfully by VEDA. The HOMO/LUMO energy gap emphasizes adequate charge transfer happening within the molecule. A study of donor-acceptor interconnections was done via NBO analysis. MEP surface analysis was done to demonstrate charge distribution and reactive areas qualitatively in the molecule. The degree of relative localization of electrons was analyzed via ELF Diagram. The Fukui function analysis showed possible sites for attacks by different substituents. By using the TD-DFT method and PCM solvent model, the UV–Vis spectrum (gas, methanol, DMSO) and the maximum absorption wavelength was computed and compared with experimental data. 3D and 2D intermolecular interactions in the crystal were analyzed via Hirshfeld surface analysis and fingerprint plots reveal that the EAMC crystal was stabilized by H–-H/H–-H/C–-H bond formation. The molecular docking was done with 7 different protein receptors on the molecule to find the best ligand-protein interactions. Molecular dynamic simulations and MMGBSA calculations were also carried out to find out the best binding of the ligand with the protein. Communicated by Ramaswamy H. Sarma

Reversed bond-slip model of deformed bar embedded in concrete based on ensemble learning algorithm

A reversed bond-slip relationship that simultaneously considers key factors, such as the concrete cover, stirrups, fiber content, and lateral pressure is required to simulate the seismic response of reinforced concrete structures. In this study, the features of the hysteresis curves with different bond conditions and loading histories were discussed and analyzed, and a corresponding bond stress-slip model based on an ensemble learning (EL) algorithm, XGBoost, was then established. In this model, 10 key factors were selected as the input parameters and 4 reversed bond parameters were selected as the output results. During the training and testing process, a total of 901 sets of experimental data were collected and were randomly split into a training set and testing set at a ratio of 8:2. Compared with the empirical models and two other EL algorithms, the XGBoost method presented a high accuracy to predict the bond parameters with different bond conditions, and the proposed bond stress-slip model correlated well with the test results.

Optimization of Structural Damage Repair with Single and Double-Sided Composite Patches through the Finite Element Analysis and Taguchi Method

Over the last four decades, numerous studies have been conducted on the use of bonded composite repairs for aircraft structures. These studies have explored the repair of damaged plates through experimental, numerical, and analytical methods and have found that bonded composite repairs are effective in controlling crack damage propagation in thin plates. The use of double-sided composite repairs has been found to improve repair performance within certain limits. This study focuses on these limits and optimizes double-sided composite repairs by varying adhesive bond and composite patch parameters. The optimization process begins with a finite element analysis to determine the stress intensity factor (SIF) for various variables and levels, followed by the application of the Taguchi method to find the optimal combination of parameters for maximizing the normalized SIF. In conclusion, we successfully determined the stress intensity factor (SIF) for various variations and normalized it for optimization. An optimization study was then performed using the Taguchi design and the results were analyzed. Our findings demonstrate the repair performance of bonded composite patches using a cost-effective and energy-efficient approach.

Thermally activated transformations of the dielectric response function of mono- and disaccharides in the THz range

The variety of physical and chemical properties of saccharides is determined, in particular, by their isomerism and the variability of their hydrogen bond parameters. We studied the transformation of the vibrational spectra of mono- and disaccharides using pulsed terahertz spectroscopy in a wide temperature range. The stability ranges of saccharides were determined from the temperature dependences of the vibrational spectra and resonance parameters. The revealed difference in frequencies and intensities of vibrational modes of the hydroxyl groups in different saccharides correlate with the parameters of hydrogen bonds. Based on the data over a wide temperature range, it was found that the anharmonicity of vibrational modes appears in the form of coupling between resonances and the formation of wide asymmetric bands. Temperature square dependence of the resonance eigenfrequencies in the disaccharides has been revealed.

Mn(II) assisted synthesis of N-phenyl-5-(pyridin-3-yl)-1,3,4-oxadiazol-2-amine and evaluation of its antiproliferative activity

The global burden of cervical cancer is continuously increasing day by day affecting the world population. Wide arrays of agents are prevalent for the treatment of this chronic disease but the survival rates are still limited. The titled compound N-phenyl-5-(pyridin-3-yl)-1,3,4-oxadiazol-2-amine (Pypao) was prepared through the cyclization of nicotinoyl-N-phenyl hydrazine carbothioamide catalyzed by manganese (II) acetate. Uv-Vis, IR, NMR, elemental analyses, and single-crystal X-ray data were utilized for the description of the compound Pypao. The crystal structure of Pypao is stabilized via intermolecular hydrogen bonding interactions, which is further confirmed with Hirshfeld surface analysis. The DFT methods were also used to optimize the Pypao and obtained bond parameters have been found coherent with the experimental data. FMO and TD-DFT studies are also performed to gain insights into the electronic behavior of Pypao. Furthermore, the binding potential of Pypao to different oncoproteins of HPV namely E6, E6AP, and E7 have been examined through a molecular docking study. The in-vitro anticancer activity of Pypao has been investigated against SiHa cells. The anticancer potential of Pypao has been evaluated through various assays including MTT, DAPI stating, AO/PI staining, etc. Both time and dose-dependent activity of Pypao have been investigated.

A novel micropolar peridynamic model for rock masses with arbitrary joints

A novel micropolar peridynamic model is proposed to simulate fracture behaviors of rock masses with arbitrary joints. The rock masses are discretized into a group of material points linked through two kinds of bonds, i.e. ordinary and joint bonds, which represent the mechanical behaviors of rock block and joint, respectively. The peridynamic parameters of ordinary and joint bonds are introduced to keep the consistence of the strain energy obtained from the proposed peridynamic model and from the continuum mechanics. The stress condition of the bond in micropolar peridynamic model is defined in terms of the displacement gradients of material points. Then a new stress-based failure criterion is proposed to describe the dynamic fracture for jointed rocks. The proposed model is verified by comparing its predictions with those from experimental observations. Numerical examples demonstrate that the wave transmission and crack development process of rock masses with different joint sets are well captured by the proposed model. Moreover, the influence of the joint geometry on failure characteristics of jointed rocks with an opening is further investigated by the proposed model.

Synthesis and characterization of novel binuclear zinc complex, immobilization in nano-porous support, and its catalytic application

Binuclear zinc complex, [Zn2(L)(I)2(CH3CN)] (I) (LH2 = 1,2-phenylenebis(azaneylylidene))bis(methaneylylidene))bis(2-methoxyphenol)) was prepared and single-crystal X-ray diffraction was used to establish the structure of complex assembly. Organic acid and base were used to functionalize the nano-porous material and then binuclear Zn complex was grafted into the modified materials. Brunauer-Emmett-Teller isotherm (BET), Nuclear Magnetic Resonance (NMR), Inductively Coupled Plasma analysis (ICP), X-ray Diffraction (XRD), Fourier transform infrared spectra (FT-IR), thermogravimetric analysis (TG), Scanning electron microscope (SEM), etc., were used to characterized the synthesized nano-catalysts to check for existence of guest moiety, structural stability of the parent and modified catalysts. Catalytic performance was noticeably enhanced post modification; without catalyst, acid/base functionalized, Zn2 immobilized catalyst. Binuclear zinc immobilized on acid/base silica catalyst exhibited a maximum 95%, 89% conversion of piperidine, and 87% and 86% conversion of aniline respectively. Prior to the theoretical investigation the bond parameters of the binuclear zinc complex were measured experimentally. Time-dependent Density Functional Theory (TD-DFT) and Density Functional Theory (DFT) methods were used to calculate the molecule's UV–Vis absorption spectra at B3LYP as well as LANL2DZ and 6–31G(d)). LUMOs and HOMOs energy gap were determined from the electronic transitions to determine electrophilicity index (ω), softness (S), electronegativity (χ), hardness value (Ƞ), and chemical potential (μ), etc.

The Cambridge structural database (CSD): important resources for teaching concepts in structural chemistry and intermolecular interactions

Abstract The Cambridge Structural Database (CSD) is a repository of all published organic and metal-organic crystal structures of small molecules. These compounds have been crystallized under different conditions and have variable bond parameters and molecular landscapes. Entries in the database therefore serve as real models that can be used to illustrate structural properties such as bond angles, bond distances, torsion angles and other intra- and intermolecular interactions. This paper illustrates how the CSD programs ConQuest and Mercury can be used to search the database for 3D molecular structures to teach concepts such as molecular geometry, symmetry and group theory, organometallic chemistry and intermolecular interactions involving hydrogen bonding and Full Interaction Maps (FIMs) to explore molecular landscapes for halogen bond interactions. Results obtained from these studies are beneficial to understand and predict crystal properties as well as the structural properties of molecules and ions in crystal environments.

Effect of green solvents, molecular structure and topological studies on 4-amino-1-β-d-ribofuranosyl-1,3,5 triazin-2(1H)-one - anti-blood cancer agent

The present theoretical work interprets the optimized structure, Vibrational assignments of 4-AMINO-1-β-d-ribofuranosyl-1,3,5 triazin-2(1H)-One (4AβRT) also known by the chemical name azacitidine which has 29 atoms, examined theoretically Via DFT/6–311++G (d, p) simple position level. The spectroscopic data of 4AβRT are verified. Bond parameters are analysed by optimizing the structure in gaussian 09. The charge circulation area of the molecule in a three-dimensional manner and to distinguish the electrophilic and nucleophilic sites of the molecule is done by MESP. The HOMO-LUMO (electron donor and acceptor) is important for the stability and chemical reactivity of the compound. NBO evaluation is used to understand the bonding interlinkage of the fragments. NLO analysis has been carried out. Topological analysis (ELF, LOL, RDG) has been analysed using Multiwave function. The electronic transition of the compounds with different solvents have been investigated by the TD-DFT method. Protein-Ligand docking is performed with different cancer cell-matured proteins by using the AUTODOCK program.

Bond of FRP rods in damaged RC beams strengthened with NSM technique

In strengthening reinforced concrete (RC) elements with composite materials, the role of adherence between concrete and FRP assumes great importance as it guarantees the effectiveness of the consolidation method. In this paper the bond mechanisms between FRP rods and concrete second the Near Surface Mounted (NSM) technique have been analyzed by experimental results of investigation and a theoretical linear model. The experimental investigation consists of direct pull-out tests on RC elements with circular GFRP and CFRP rods inserted into a groove. Through pull-out tests main parameters of bond have been presented. The experimental results are compared with those obtained by the theoretical model.

Спектральные проявления механизмов межмолекулярного взаимодействия модифицированных малеимидом полиэлектролитных капсул, используемых в таргетной терапии

Mechanisms of intermolecular interaction between components of polyelectrolyte target delivery capsules and maleimide, which enhances the therapeutic action of the capsule, are investigated by quantum chemical modeling methods based on Density Functional Theory (DFT). Molecules of polymer polyelectrolyte capsule components - polyarginine and dextran sulfate and maleimide molecule are investigated. Based on calculation of molecular complexes structures and corresponding IR spectra with analysis of formed hydrogen bonds parameters it was revealed that there was a strong enough hydrogen bonding between maleimide and arginine, included in capsule composition. This allows us to conclude that modification of arginine with maleimide promotes stronger hydrogen bonding with amino acids contained in human body, which is confirmed by calculations, and gives the possibility of using maleimide as an "anchor" to hold the capsule in the tissue.

Isomerization and reaction process of N2O4(H2O) n.

Liquid propellant N2O4 is prone to absorb H2O to form an N2O4(H2O) n system during long-term storage, ultimately generating HNO3, HNO2, and other substances capable of corroding the storage tank, which will adversely affect the performance of weapons and equipment. In this work, the reaction process of the N2O4(H2O) n system is simulated using density functional theory, and the potential energy surface, the geometric configurations of the molecules, the charge distribution, and the bond parameters of the reaction course at n = 0-3 are analyzed. The results show that the potential energy of the system is lower and the structure is more stable when the H2O in the N2O4(H2O) n system is distributed on the same side. When n = 1 or 2, the reaction profiles are similar, and the systems are partly ionic, although still mainly covalently bonded. When n = 3, the charge on the trans-ONONO2 group and the ON-ONO2 bond length change abruptly to -0.503 a.u. and 2.57 Å, respectively, at which point the system is dominated by ionic bonds. At n = 2, a proton-transfer phenomenon occurs in the reaction course, with partial reverse charge-transfer from NO3 - to NO+, making the ON-ONO2 bond less susceptible to cleavage, further verifying that N2O4(H2O) n tends to afford the products directly in one step as H2O accumulates in the system.

First-principles study of the adsorption and diffusion mechanisms of lithium dendrite growth

ABSTRACT Lithium dendrite growth is an important issue in the design of lithium metal batteries (LMBs), and most relevant experimental studies lack theoretical guidance. We employ density functional theory to study the adsorption and diffusion of lithium atoms, which are two dominating factors for dendrite growth, by calculating the binding energy and potential map. Perfect, dislocation defective and heteroatom defective surfaces are considered. For a perfect surface, dendrite growth on the (110) face compared to the (200) face is dominated more by the adsorption mechanism. For dislocation defects, an extra potential barrier is found on the section of the dislocation, which might lead to uncontrolled dendrite growth. For heteroatom defects, the influence is correlated with the face direction due to the correlation between the chemical bond and cell parameters; it seems that Si, P and B are unfavourable, while F, Cl and alkali metal atoms are favourable for dendrite-free LMBs.

Optimization of Shear Bonds of the Grouted Joints of Offshore Wind Turbine Tower Based on Plastic Damage Model

In recent years, offshore wind power has been developing rapidly, and single piles are among the commonly used foundations for wind turbines. Presently, experimental studies of the grouted connections of pile foundations are limited to the study of scaler models. Numerical simulations are more suitable for the mechanical analysis of the full-size structure instead of experimental ones. In numerical simulations, the linear elasticity model is widely adopted, but the plastic damage is studied scarcely. So, shear bond parameter research concerning grouted joints needs to be supplemented. In this paper, a bilinear random-motion reinforcement model based on the classical metal plasticity theory is adopted for steel, and the model for the grouting material is based on the Sidiroff energy equivalence principle. The plastic damage model for the grouted connecting section is established; the stresses and deformation distribution of the steel pipes and grout in the connecting section are analyzed using the changed shear bond parameters. The results show that the rectangular and triangular shear bonds are more reasonable than the semicircular shear bond transfer. Increasing the height of the shear bond may reduce the maximum stress and the maximum vertical displacement of the grout, and the shear bond width change has less influence on the joint bond stress and displacement.

Nanoscale synthesis, structural elucidation, DFT, and biological activity of amide appended transition metal(II) macrocyclic complexes in drug delivery system

Nanoscale complexes of Mn(II), Ni(II), and Cu(II) with 6,15-diamino-1,4,9,12-tetraazacyclohexadecane-5,8,13,16-tetraone were synthesized by ultrasonic sonication method. The Fourier-transform infrared (FTIR) spectroscopy, ultraviolet–visible (UV–vis) spectroscopy, carbon, hydrogen, and nitrogen elemental (CHN) analysis, mass spectrometry (MS), and electron spin resonance (ESR) spectroscopy were used to identify and suggest the structure of the synthesized nanocomplexes. The field emission scanning electron microscopy (FE-SEM) and powder X-ray diffraction (PXRD) revealed that the size of the synthesized nanocomplexes was 44–58 nm. Based on these studies, hexagonal, monoclinic, and cubic unit cell structure has been proposed for the synthesized Mn(II), Ni(II), and Cu(II), respectively. The theoretical calculations of the synthesized nanocomplexes were carried out by a GAUSSIAN 09 program involving geometry optimization and bond parameters using the B3LYP method. Moreover, binding energy, HOMO, and LUMO have been calculated. In addition, hardness, softness, chemical potential, and dipole moment were calculated for ligand and its metal nanocomplexes. The biological efficacy of the synthesized nanocomplexes was examined and found to be better and highly effective drug delivery system (DDS) for the antimicrobial and antioxidative agent.

Calculations of molecular properties of 2-(2'-hydroxyphenyl)benzoxazole by semi-empirical tight-binding methods

The semi-empirical tight-binding methods GFN1-xTB and GFN2-xTB are applied to calculations of structure, energy and normal vibrations of the molecule of 2-(2'-hydroxyphenyl)benzoxazole undergoing excited state intramolecular proton transfer. The results are compared with ones obtained by the density-functional tight-binding methods with hydrogen interaction corrections and density functional theory. The GFN2-xTB method is found to provide good correspondence to the results obtained by more accurate but much slower density functional theory method for geometrical parameters of hydrogen bond, relative energy of molecular conformations and potential energy surface.

Synthesis, Spectroscopic, Computational, Biological and Molecular docking studies on 3‐allyl 2,6‐diaryl piperidin‐4‐ones

AbstractA series of 3‐allyl‐2,6‐diarylpiperidin‐4‐one derivatives were designed and synthesized as antimicrobial agents with good yields. The target compounds were characterized by Mass, NMR, FT‐IR and FT‐Raman spectral techniques. The optimization had been performed on the title compound using the B3LYP method with 6‐311++G(d,p) basis set. The optimized bond parameter of the title molecule was calculated by DFT method. To study the intramolecular charge transfer within the molecule, the Lewis (bonding) and Non‐Lewis (anti‐bonding) structural calculation was performed. The Non‐linear optical behaviour of the title compound was measured using first order hyperpolarizability calculation. Mulliken atomic charges and thermodynamic properties were also calculated and analyzed. In vitro antibacterial and antifungal screening for all the synthesized 3‐allyl 2,6‐diaryl piperidin‐4‐ones was evaluated for two Gram‐positive bacteria (Staphylococcus aurous, Enterococcus faecalis), three Gram‐negative bacteria Pseudomonas aeruginosa, Escherichia coliand K. pneumonia) and five fungi (Candida albicans, Aspergillus niger, Aspergillus flavus, Rhizopus sp and Mucor sp). All the compounds showed good antibacterial and antifungal activities. Molecular docking study is to demonstrate that piperidine derivatives bind to Ribonucleotide reductases (RNRs) enzymes and to evaluate whether these molecules can be used as potential drugs.

Improved microwave dielectric characteristics in CaHf1−xTixO3 ceramics

AbstractIn the present work, effects of Ti‐substitution for Hf upon microwave dielectric characteristics for CaHfO3 ceramics were investigated. CaHf1−xTixO3 solid solution in space group Pnma was determined in the present ceramics with x = 0–0.075, and only minor amount of secondary phases of CaHfO3 (R, 1.3 wt%) and Ca2Hf7O16 (R, 0.8 wt%) was detected. The significantly improved microwave dielectric characteristics were achieved with Ti‐substitution in CaHfO3 ceramics. With increasing x, the temperature coefficient of resonant frequency τf was substantially tuned from negative to positive through zero, which was caused by the decrease of oxygen octahedral tilting, and the Qf value was apparently improved simultaneously and reached the maximum of 43670 GHz at x = 0.025, while the dielectric constant εr increased monotonously. The remarkable improvement of Qf was attributed to the enhancement of octahedral framework rigidity and the decreased nonuniform distribution of inner chemical bonding in crystal based on the change of chemical bond parameters calculated by the Phillips–Van Vechten–Levine bond theory, which was further confirmed by the higher frequency and narrower width of stretch mode of octahedron (i.e., A1g(O) near 730 cm−1) in Raman spectra. An interesting phenomenon was found in titanium‐containing perovskite ceramics that they had consistent trend of τf changing with tolerance factor, which was helpful to design temperature‐stable perovskite microwave dielectric ceramics. The best combination of microwave dielectric characteristics was achieved at x = 0.035: εr = 27.2, Qf = 42 870, and τf = +3 ppm/°C. For practical applications of the present ceramics, further improvement of Qf is required, and it is expected to be achieved through microstructure optimization.

Revealing the structure of the sodium-leached layer of soda lime silica glass: A comprehensive spectroscopic analysis

Acid treatment of soda lime silica glass results in incongruent leaching of sodium from the surface, with minimal dissolution of the silicate network or the other cationic network modifiers. The structure of this sodium-leached region was probed using nanoscale-FTIR and Raman spectroscopy. After accounting for interfacial interference, the resultant spectra were compared with molecular dynamics simulations to connect the observed spectral changes to the structure. This comparison showed that the correlations between spectral features and bond parameter distributions derived from the melt-quench formed glass can also be applied to a chemically-modified glass. Additionally, the IR active shoulder at ∼950 cm-1 which was traditionally attributed to the non-bridging oxygen stretch mode, was confidently correlated to perturbations in the silicate network which results from the network modifiers which charge compensate those non-bridging oxygen. The decrease in this spectral feature after acid treatment then corresponds to localized structural relaxations as the glass network becomes more silica-like.

Structure of an amorphous calcium carbonate phase involved in the formation of Pinctada margaritifera shells.

Some mollusc shells are formed from an amorphous calcium carbonate (ACC) compound, which further transforms into a crystalline material. The transformation mechanism is not fully understood but is however crucial to develop bioinspired synthetic biomineralization strategies or accurate marine biomineral proxies for geoscience. The difficulty arises from the simultaneous presence of crystalline and amorphous compounds in the shell, which complicates the selective experimental characterization of the amorphous fraction. Here, we use nanobeam X-ray total scattering together with an approach to separate crystalline and amorphous scattering contributions to obtain the spatially resolved atomic pair distribution function (PDF). We resolve three distinct amorphous calcium carbonate compounds, present in the shell of Pinctada margaritifera and attributed to: interprismatic periostracum, young mineralizing units, and mature mineralizing units. From this, we extract accurate bond parameters by reverse Monte Carlo (RMC) modeling of the PDF. This shows that the three amorphous compounds differ mostly in their Ca-O nearest-neighbor atom pair distance. Further characterization with conventional spectroscopic techniques unveils the presence of Mg in the shell and shows Mg-calcite in the final, crystallized shell. In line with recent literature, we propose that the amorphous-to-crystal transition is mediated by the presence of Mg. The transition occurs through the decomposition of the initial Mg-rich precursor into a second Mg-poor ACC compound before forming a crystal.