Molecular Structure Calculations Research Articles

Aqueous extract of CAP-ash: A greener benchmark for Suzuki-Miyaura coupling reaction in palladium catalyzed ligand-free condition

Synthesis, molecular, spectroscopic properties, and electronic structure calculations of biphenyls derivatives have been achieved using a highly efficient catalytic amount of Pd(OAc)2 in aqueous extract of custard apple peels (CAP)-ash (AECAP) a green, highly cost-effective, operationally convenient and environmentally benign media at ambient temperature. The analytical reports showed the presence of metal oxides which are probably extracted in water produces corresponding hydroxides, which provide alkaline media in water which shows dual performance (solvent and base) for said cross-coupling transformation. The catalytic system is generated in situ based on aqueous extract and Pd(OAc)2 which requires no external base and ligand. Moreover, the study also offers insights into the frontier molecular orbitals (FMO), electronegativity, chemical potential, global electrophilicity index, ionization potential, electron affinity, chemical hardness, and softness properties of the synthesized biphenyl derivatives for understanding their stability, active sites, and biological activity using density functional theory (DFT) at the B3LYP/6–311G(d,p) level/basis.

Study on low-rank coal flotation collector screening and performance based on molecular polarity index.

Extensive studies using a trial-and-error approach have been conducted on low-rank coal flotation collectors. However, screening efficient collectors remains a considerable challenge due to the lack of suitable screening principles. It has proven that polar compounds such as carboxylic acids and esters are effective collectors for low-rank coal flotation. In this work, the effects of carboxylic acid, alcohol, and methyl ester on the floatability of low-rank coal were compared, the flotation performance of the polar collector was evaluated with theoretical calculations, a suitable evaluation parameter was determined and a screening principle based on this parameter was determined. The results show that the enhancement effects of polar collectors on low-rank coal floatability follow the order of methyl decanoate > methyl laurate > methyl octanoate > sec-octanol > methyl oleate (or methyl oleate > sec-octanol) > n-octanoic acid. Compared with the molecular polarity index, the hydrophobicity indices log P and dipole moment cannot be used to accurately evaluate different types of collectors and the same type of collectors, respectively. At room temperature, liquid polar compounds with molecular polarity indices in the range of 6.0 ~ 8.0kcal/mol effectively enhance the floatability of low-rank coal. The molecular polarity index of the collector is used for the first time to screen effective collectors of low-rank coal in this work. This parameter is anticipated to be highly important for the development and research of low-rank coal and other mineral collectors. To obtain reasonable and accurate molecular structure, geometry optimization and frequency calculations of the studied collectors were conducted via the Gaussian 09 software package based on density functional theory at the B3LYP/6-311 + G (d, p) level. The integral equation formalism for the polarizable continuum model (IEF-PCM) was utilized with water as the solvent (dielectric constant = 78.36, T = 298K) for all the calculations. Then, the atomic charge distributions (MPA and NPA) and electrostatic potential maps, the dipole moment and molecular polarity index, and the log P and water solubilities of studied collectors were shown or calculated by Gauss View 5.0, Mutiwfn program and website ( https://www.molsoft.com/mprop/mprop.cgi ), respectively.

Graph Neural Networks in Point Clouds: A Survey

With the advancement of 3D sensing technologies, point clouds are gradually becoming the main type of data representation in applications such as autonomous driving, robotics, and augmented reality. Nevertheless, the irregularity inherent in point clouds presents numerous challenges for traditional deep learning frameworks. Graph neural networks (GNNs) have demonstrated their tremendous potential in processing graph-structured data and are widely applied in various domains including social media data analysis, molecular structure calculation, and computer vision. GNNs, with their capability to handle non-Euclidean data, offer a novel approach for addressing these challenges. Additionally, drawing inspiration from the achievements of transformers in natural language processing, graph transformers have propelled models towards global awareness, overcoming the limitations of local aggregation mechanisms inherent in early GNN architectures. This paper provides a comprehensive review of GNNs and graph-based methods in point cloud applications, adopting a task-oriented perspective to analyze this field. We categorize GNN methods for point clouds based on fundamental tasks, such as segmentation, classification, object detection, registration, and other related tasks. For each category, we summarize the existing mainstream methods, conduct a comprehensive analysis of their performance on various datasets, and discuss the development trends and future prospects of graph-based methods.

On the Spectroscopy of Phosphaalkynes: Millimeter- and Submillimeter-Wave Study of C2H5CP.

Ethyl phosphaethyne, C2H5CP, has been characterized spectroscopically in the gas phase for the first time, employing millimeter- and submillimeter-wave spectroscopy in the frequency regime from 75 to 760 GHz. Spectroscopic detection and analysis was guided by high-level quantum-chemical calculations of molecular structures and force fields performed at the coupled-cluster singles and doubles level extended by a perturbative correction for the contribution from triple excitations, CCSD(T), in combination with large basis sets. Besides the parent isotopologue, the three singly substituted 13C species were observed in natural abundance up to frequencies as high as 500 GHz. Despite the comparably low astronomical abundance of phosphorus, phosphaalkynes, R-CP, such as C2H5CP are promising candidates for future radio astronomical detection.

Effects of intramolecular hydrogen bonding on nuclear magnetic resonance, electron paramagnetic resonance and molecular docking studies: Mexiletine molecule.

In this study, the molecular structure of the mexiletine molecule was investigated. Since the Mexiletine molecule is a drug active ingredient, its molecular structure and spectroscopic properties are important. The effects of intramolecular hydrogen bonding on Nuclear Magnetic Resonance Parameters (NMR), Electron Paramagnetic Resonance (EPR) parameters and molecular docking studies were examined in the mexiletine molecule. The effects of intramolecular hydrogen bonding on EPR parameters and molecular docking studies are the most important steps for this study. Conformational space scanning required for molecular structure calculations was carried out with the Molecular Mechanic Force Field method. DFT method with 6-311 + + G(d,p) basis set level was used to obtain the most stable structure among the conformations. NMR parameters (1H and 13C chemical shift values) were also performed using the same basis set as the DFT method. The radicals created to calculate the Electron Paramagnetic Resonance parameters were modeled using the DFT/B3LYP/6-311 + + G(d,p) method basis set level. Molecular Docking studies were carried out with the Autodock vina program.

Algebraic Solution of Gaunt Coefficients via the Angular Momentum Ladder Operators

In this study, Gaunt coefficients, frequently encountered in quantum mechanical calculations of atomic and molecular structures, have been algebraically derived. Firstly, the Gaunt coefficient, equal to the integral over the solid angle of the product of three spherical harmonics, is written in terms of angular momentum ladder operators. Subsequently, raising or lowering operators are applied to spherical harmonics, and the obtained integrals are solved using the recurrence and orthogonality relations of spherical harmonics. As a result, algebraic expressions for Gaunt coefficients are obtained in terms of quantum numbers.

Gas-Pressurized Torrefaction of Lignocellulosic Solid Wastes: Deoxygenation and Aromatization Mechanisms of Cellulose.

A novel gas-pressurized (GP) torrefaction method at 250 °C has recently been developed that realizes the deep decomposition of cellulose in lignocellulosic solid wastes (LSW) to as high as 90% through deoxygenation and aromatization reactions. However, the deoxygenation and aromatization mechanisms are currently unclear. In this work, these mechanisms were studied through a developed molecular structure calculation method and the GP torrefaction of pure cellulose. The results demonstrate that GP torrefaction at 250 °C causes 47 wt.% of mass loss and 72 wt.% of O removal for cellulose, while traditional torrefaction at atmospheric pressure has almost no impact on cellulose decomposition. The GP-torrefied cellulose is determined to be composed of an aromatic furans nucleus with branch aliphatic C through conventional characterization. A molecular structure calculation method and its principles were developed for further investigation of molecular-level mechanisms. It was found 2-ring furans aromatic compound intermediate is formed by intra- and inter-molecular dehydroxylation reactions of amorphous cellulose, and the removal of O-containing function groups is mainly through the production of H2O. The three-ring furans aromatic compound intermediate and GP-torrefied cellulose are further formed through the polymerization reaction, which enhances the removal of ketones and aldehydes function groups in intermediate torrefied cellulose and form gaseous CO and O-containing organic molecules. A deoxygenation and aromatization mechanism model was developed based on the above investigation. This work provides theoretical guidance for the optimization of the gas-pressurized torrefaction method and a study method for the determination of molecular-level structure and the mechanism investigation of the thermal conversion processes of LSW.

Theoretical process for the investigation of dielectric characteristics of F3NO as an alternative gas for SF6

To examine the possibility of using a gas molecule as an SF6 alternative gas, the insulation properties of the molecule must be estimated. In this work, we present a theoretical approach to calculate geometry parameters, electron scattering cross sections, and transport properties of nitrogen fluoride oxide (F3NO), which we have selected as an alternative to SF6. The molecular minimum structure of F3NO was optimized using the ɷB97X-D functional combined with the aug-cc-pVTZ basis set. Using this initial geometry obtained by the molecular structure calculation, the R-matrix calculation was done to obtain the elastic and momentum transfer cross section. The BE-f method was used for electronic excitation cross section. For the ionization cross section, the binary encounter Bethe method was used. From the calculated cross section data, the electron transport coefficients and reaction coefficients were calculated by solving the two-term approximated Boltzmann equation to investigate the discharge and insulation characteristics.

Reactivity properties of the HOSO and HSO2 isomers in liquid medium: a sequential Monte Carlo/quantum mechanics study.

The rationalization of acid rain formation steps is fundamental for mitigating its effects. It is believed the hydroxysulfinyl radical is an intermediate species for the production of atmospheric sulfuric acid. Two stable configurations HOSO and HSO2 have been reported for such a radical in the gas phase. This work aims at studying these isomers in the aqueous medium. The electrical and reactivity quantities - electronic chemical potential ([Formula: see text]), chemical hardness ([Formula: see text]), and electrophilicity ([Formula: see text]) - are here calculated and compared. Considering first solvation shells (15H2O for HSO2 and 23H2O for HOSO), an increase of 25% in the dipole moment of HSO2 was obtained, while the dipole moment of HOSO decreases in 11%. Both solvated isomers grow softer ([Formula: see text] decreases) contrasted to the gas phase. HOSO and HSO2 are studied through a sequential Monte Carlo/quantum mechanics approach. Lennard-Jones plus the Coulomb potentials were used to represent intermolecular potential interaction in the frame of the DICE package. Molecular structure calculations were performed at CASPT2/aug - cc - pV(T + d)Z level of theory using the MOLPRO suite of programs.

New analysis of the [formula omitted]C[formula omitted]O[formula omitted] (B[formula omitted] - X[formula omitted]) system: Spin-orbit and spin-rotation coupling of the X[formula omitted] state

In the present work a new experimental and theoretical analysis of the B2Σ+→ X2Σ+ system of the molecular ion 12C16O+ is performed. New transitions regarding the vibrational levels v′=4 of the B2Σ+ electronic state and the vibrational level v″=7 of the electronic state X2Σ+ have been recorded. For rationalising the experimental observations, molecular structure calculations were carried out and, from them, a detailed investigation about the fine structure of rotational levels of the X2Σ+ could be performed. For such, the spin-rotational constant, γ, is characterised through the Δg⊥ calculation, the perpendicular component of the electronic g-tensor, in combination with Curl’s relation. At equilibrium geometry, the present Δg⊥ is computed using the multireference configuration interaction wavefunction to be −2430 ppm in agreement with the experimental one [−2344 ppm]. The R-dependence of the g-tensor has been explored in order to estimate the theoretical γv (v=0–7). In addition, the importance of the lowest Π states in this kind of calculation is widely discussed. A comparison between experiment and theory is presented, validating our findings and the methodology employed in our analysis.

Study on crystal structure, spectroscopic, thermodynamic properties and Hirshfeld surfaces of a new spirocompound containing thiourea group C17H18N2O4S

A new spirocompound containing thiourea group 1-((2,4-dioxo-1,5-dioxaspiro[5.5]undecan-3-ylidene)methyl)-3-phenylthiourea (DMP) was designed and obtained. The compound (DMP) was confirmed using the single X-ray diffraction, 1H NMR and 13C NMR, IR, Raman, MS and UV–Vis. The DFT calculations of molecular structure, infrared and Raman spectroscopy and electronic transition were performed using the two different levels of B3LYP/cc-pVDZ/ and B3LYP/6–311G(d, p). The theoretical results match with the experimental ones. The gap energy of HOMO and LUMO of DMP was 3.88 eV. The DMP is thermally stable up to 200 °C according to the data obtained from TG analysis. Finally, the Mulliken population analysis, Hirshfeld surfaces analysis, MEP, NLO and NBO of DMP were discussed.

Application of Machine Learning to the Design of Energetic Materials: Preliminary Experience and Comparison with Alternative Techniques

AbstractThe last few years have seen a steep rise in the use of data‐driven methods in different scientific fields historically relying on theoretical or empirical approaches. Chemistry is at the forefront of this paradigm shift due to the longstanding use of computational tools involved in the calculation of molecular structures and properties. In this paper, we showcase examples from the literature as well as work in progress in our lab in order to give a brief overview on how these methods can benefit the energetic materials community. A deep learning approach is compared to “traditional” QSPR and semi‐empirical approaches for molecular property prediction, and specificities inherent to energetic materials are discussed. Deep generative models for the design of new energetic materials are also presented. We conclude by giving our view on the most promising strategies for future in silico generation of new energetic materials satisfying the performance/sensitivity trade‐off.

Topological data analysis of protein structure and inter/intra-molecular interaction changes attributable to amino acid mutations

The presence of some amino acid mutations in the amino acid sequence that determines a protein’s structure can significantly affect that 3D structure and its biological function. However, the effects upon structural and functional changes differ for each displaced amino acid, and it is very difficult to predict these changes in advance. Although computer simulations are very effective at predicting conformational changes, they struggle to determine whether the amino acid mutation of interest induces sufficient conformational changes, unless the researcher is a specialist in molecular structure calculations. Therefore, we created a framework that efficiently utilizes molecular dynamics and persistent homology methods to identify amino acid mutations that induce structural changes. We show that this framework can be used not only to predict conformational changes produced by amino acid mutations but also to extract groups of mutations that significantly alter similar molecular interactions, by capturing the resultant protein–protein interaction changes.

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.

Exploring proten’s conformational space by using encoding layer supervised auto-encoder

Protein function is related to its structure and dynamic change. Molecular dynamics simulation is an important tool for studying protein dynamics by exploring its conformational space, however, conformational sampling is a nontrivial issue, because of the risk of missing key details during sampling. In recent years, deep learning methods, such as auto-encoder, can couple with MD to explore conformational space of protein. After being trained with the MD trajectories, auto-encoder can generate new conformations quickly by inputting random numbers in low dimension space. However, some problems still exist, such as requirements for the quality of the training set, the limitation of explorable area and the undefined sampling direction. In this work, we build a supervised auto-encoder, in which some reaction coordinates are used to guide conformational exploration along certain directions. We also try to expand the explorable area by training through the data generated by the model. Two multi-domain proteins, bacteriophage T4 lysozyme and adenylate kinase, are used to illustrate the method. In the case of the training set consisting of only under-sampled simulated trajectories, the supervised auto-encoder can still explore along the given reaction coordinates. The explored conformational space can cover all the experimental structures of the proteins and be extended to regions far from the training sets. Having been verified by molecular dynamics and secondary structure calculations, most of the conformations explored are found to be plausible. The supervised auto-encoder provides a way to efficiently expand the conformational space of a protein with limited computational resources, although some suitable reaction coordinates are required. By integrating appropriate reaction coordinates or experimental data, the supervised auto-encoder may serve as an efficient tool for exploring conformational space of proteins.

Poli (ɛ-Kaprolakton)’ un Yapısı ve Elektronik Özelliklerinin Yoğunluk Fonksiyonel Yöntemiyle Teorik Bir Çalışması

The purpose of this research is to determine the structure's electrophilic and nucleophilic character by examining at local and global chemical activity factors. The electronic behavior of Poly (ɛ-caprolactone) was investigated by theoretical quantum chemical computation for this purpose. Natural Bonding Orbital (NBO) analysis is a powerful technique for studying stabilization energy E(2), conjugated interactions, and charge transfer in quantum chemistry molecular systems. Furthermore, dipole moment, polarizability, and hyper polarizability characteristics were used to determine the structure's nonlinear optics (Nonlinear Optical, NLO) features. All the theoretical calculations of molecular structure were calculated via the Density Functional Theory (DFT) method in the B3LYP level and STO-3G basis set.

Best-Practice DFT Protocols for Basic Molecular Computational Chemistry.

Nowadays, many chemical investigations are supported by routine calculations of molecular structures, reaction energies, barrier heights, and spectroscopic properties. The lion's share of these quantum-chemical calculations applies density functional theory (DFT) evaluated in atomic-orbital basis sets. This work provides best-practice guidance on the numerous methodological and technical aspects of DFT calculations in three parts: Firstly, we set the stage and introduce a step-by-step decision tree to choose a computational protocol that models the experiment as closely as possible. Secondly, we present a recommendation matrix to guide the choice of functional and basis set depending on the task at hand. A particular focus is on achieving an optimal balance between accuracy, robustness, and efficiency through multi-level approaches. Finally, we discuss selected representative examples to illustrate the recommended protocols and the effect of methodological choices.

Best‐Practice DFT Protocols for Basic Molecular Computational Chemistry**

AbstractNowadays, many chemical investigations are supported by routine calculations of molecular structures, reaction energies, barrier heights, and spectroscopic properties. The lion's share of these quantum‐chemical calculations applies density functional theory (DFT) evaluated in atomic‐orbital basis sets. This work provides best‐practice guidance on the numerous methodological and technical aspects of DFT calculations in three parts: Firstly, we set the stage and introduce a step‐by‐step decision tree to choose a computational protocol that models the experiment as closely as possible. Secondly, we present a recommendation matrix to guide the choice of functional and basis set depending on the task at hand. A particular focus is on achieving an optimal balance between accuracy, robustness, and efficiency through multi‐level approaches. Finally, we discuss selected representative examples to illustrate the recommended protocols and the effect of methodological choices.

Solid-State Conformational Isomerism Lacking a Gas-Phase Energy Barrier: Its Structural, Spectroscopic, and Theoretical Identification in an Organochromium(III) Complex

We present a combined X-ray diffraction (XRD), high-frequency and -field electron paramagnetic resonance (HFEPR), and theoretical study of an organochromium(III) complex with relevance to polymerization catalysis that crystallizes in a disordered structure with two conformational isomers in a ratio of 0.89:0.11. The structure is exceptional, as the disorder is restricted to the CrCl2 moiety, whereas the organic ligand is not disordered within the precision of the structure determination. Although the geometry is only slightly varied, these Cr(III) (3d3, S = 3/2) isomers give substantially different EPR spectra so that both species can be analyzed in terms of distinct zero-field splitting (zfs) parameters. Using the solid-state molecular structure of each isomer, calculated spin Hamiltonian parameters using high-level ab initio methods are in good accordance with the experimental results. However, no energy barrier could be identified by calculation of the gas-phase molecular structure, leading to the conclusion that the occurrence of the two isomers is due to intermolecular interactions in the solid state. These results highlight the subtle structural differences that can exist in organometallic complexes. Such structural conformations might well be accessible in solutions of precatalysts and active polymerization catalysts affecting their reactivity.

Architecture of a dinuclear Co(II) complex based on 3-amino-1,2,4-triazole-5-carboxylic acid: molecular structure, thermal behavior, optical properties, and DFT calculations

The dinuclear compound [Co2(Hatzc)2(H2O)6](NO3)2·4H2O containing the polytopic ligand Hatzc‒ = 3-amino-4H-1,2,4-triazole-5-carboxylate was synthesized and characterized. Single-crystal X-ray diffraction showed that two monoanionic N,O-chelating Hatzc‒ ligands bridge two Co(II) ions in a µ-N1,N2 fashion. Both Co(II) centers are further coordinated by three H2O ligands making up an octahedral coordination. A complex network of intra- and intermolecular O‒H···O and N‒H···O hydrogen bonding interactions characterize the structure. Hirshfeld surface analysis, ATR–FTIR, and FT-Raman spectroscopy in combination with density functional theory (DFT) calculation of vibrational modes confirm this multitude of H bonds. Thermogravimetric and differential thermal analysis experiments under an argon atmosphere in the temperature range of 25–900 °C showed thermal stability till about 100 °C and multi-step decomposition yielding Co2O3 at about 280 °C. The octahedral environment of Co(II) was confirmed by UV–vis absorption spectroscopy, which shows weak absorption bands at around 520 nm assignable to electronic d‒d transitions alongside with π‒π* transitions dominating the 250–350 nm range. Time-dependent DFT calculated excited states agree very well in terms of energy match with the observed transitions. The direct and indirect optical band gap values were determined using the Tauc plot method to 3.33 eV and 2.75 eV, respectively, indicating semiconducting properties.