Calculations Of Complexes Research Articles

PKaH values and θH angles of phosphanes to predict their electronic and steric parameters.

Phosphanes play an important role in various applications, serving as a class of organic bases with basicities spanning more than 30 orders of magnitude. Accessing comprehensive basicity data for phosphanes has been challenging due to scattered information across multiple sources and notable gaps in the existing data. In this report, we present basicities (pKaH values) of a diverse set of phosphanes, both newly measured or calculated and collected from the literature. We demonstrate that pKaH values can serve as an alternative to Tolman electronic parameters (TEP values) in evaluating the electronic properties of phosphanes. Additionally, we suggest parameters for assessing the steric properties of phosphanes without the need for preparation or calculation of metal-ligand complexes.

Crystal structure and electronic structure calculations of a novel organic triphosphate complex: excellent electrochemical properties with ultra-efficient lithium storage capacity

A new organic–inorganic hybrid molecule, cyclohexyl ammonium dihydride triphosphate, was synthesized at room temperature with slow evaporation, yielding a new triphosphate complex HO10P3·(C6H14N)4·2(H2O) using the chemical ion exchange process.

Investigation of Coordination Compounds of Gadolinium (III) With b-Diketones

New coordination compounds of gadolinium with -diketones containing unsaturated and aliphatic or aromatic substituents in the -positions of the chelate ring have been synthesized. The performed quantum-chemical calculations of ligand molecules indicate the best acceptor properties of ligands with aromatic substituents. An analysis of the IR spectra and quantum chemical calculations of the metal complexes indicates the bidentate-chelate coordination of the ligand molecules and their arrangement in different planes, regardless of the nature and geometric structure of the substituent in the β-diketone molecule. The energies of the triplet levels of the ligands are calculated. The morphology and dispersion of the synthesized metal complexes have been studied.

Modelling of structure and concentration characteristics of water-alcohol solutions

Water-alcohol solutions are widely used in pharmacy, food industry, engineering, etc. The study of their physical and chemical properties has a long history. Nevertheless, due to the complexity of these systems, there is still an interest in their research stimulated by the development of biochemistry in terms of the study and protection of the environment, global climate change, renewable energy resources and cosmochemistry. The purpose of the presented study is the quantum-chemical investigation of water clusters with methyl and ethyl alcohol molecules, as well as the modelling of concentration dependences of the excess molar volume of ethyl alcohol solution in water at different temperatures. Based on quantum-chemical calculations of paired and mixed complexes of water with methanol and ethanol, taking into account solvation effects, study reveals the formation of thermodynamically efficient complexes in liquid, in contrast to the ideal gas state, while in the mixture both individual solvated alcohol molecules and complexes will be in equilibrium. We noted a relative difference in the free energies of solvation of paired and mixed methanol and ethanol complexes. The paper proposes a technique for calculating the excess molar volume in water-alcohol mixtures by approximating the experimental dependences by Lejandre polynomials of the ninth degree. The calculation results showed high accuracy. Hence, continuous functions describe the dependences of the calculated coefficients of Lejandre polynomials on temperature.

Моделирование структуры и концентрационных характеристик водно-спиртовых растворов

Water-alcohol solutions are widely used in pharmacy, food industry, engineering, etc. The study of their physical and chemical properties has a long history. Nevertheless, due to the complexity of these systems, there is still an interest in their research stimulated by the development of biochemistry in terms of the study and protection of the environment, global climate change, renewable energy resources and cosmochemistry. The purpose of the presented study is the quantum-chemical investigation of water clusters with methyl and ethyl alcohol molecules, as well as the modelling of concentration dependences of the excess molar volume of ethyl alcohol solution in water at different temperatures. Based on quantum-chemical calculations of paired and mixed complexes of water with methanol and ethanol, taking into account solvation effects, study reveals the formation of thermodynamically efficient complexes in liquid, in contrast to the ideal gas state, while in the mixture both individual solvated alcohol molecules and complexes will be in equilibrium. We noted a relative difference in the free energies of solvation of paired and mixed methanol and ethanol complexes. The paper proposes a technique for calculating the excess molar volume in water-alcohol mixtures by approximating the experimental dependences by Lejandre polynomials of the ninth degree. The calculation results showed high accuracy. Hence, continuous functions describe the dependences of the calculated coefficients of Lejandre polynomials on temperature.

Crystal Chemistry and Structural Complexity of the Uranyl Molybdate Minerals and Synthetic Compounds

This paper reviews not the largest, but at the same time quite an interesting, group of natural and synthetic uranyl molybdate compounds. Nowadays, nine minerals of U and Mo are known, but the crystal structures have only been reported for five of them. Almost an order of magnitude more (69) synthetic compounds are known. A significant discrepancy in the topological types for natural and synthetic phases is shown, which is most likely due to elevated temperatures of laboratory experiments (up to 1000 °C), while natural phases apparently grow at significantly lower temperatures. At the same time, the prevalence of dense topologies (with edge-sharing interpolyhedral linkage) among natural phases can be noted, which is fully consistent with other recently considered mineral groups. Uranyl molybdates demonstrate several similarities with compounds of other U-bearing groups; however, even topological matches do not lead to the appearance of completely isotypic compounds. Structural complexity calculations confirm, in general, crystal chemical observations. Considering the prevalence of dense structures in which coordination polyhedra of uranium and molybdenum are connected through common edges as well as framework architectures, one can expect a less significant influence of interlayer species on the formation of the crystal structure than the main U-bearing complexes. The more structural complexity of the uranyl molybdate units, the more complex of the entire crystal structure is. In addition, there is a tendency for complexity to increase with increasing density of the complex; the simplest structures are vertex-shared, while the complexity increases with the appearance of common edges.

A Rigorous Framework for Calculating Protein-Protein Binding Affinities in Membranes.

Calculating the binding free energy of integral transmembrane (TM) proteins is crucial for understanding the mechanisms by which they recognize one another and reversibly associate. The glycophorin A (GpA) homodimer, composed of two α-helical segments, has long served as a model system for studying TM protein reversible association. The present work establishes a methodological framework for calculating the binding affinity of the GpA homodimer in the heterogeneous environment of a membrane. Our investigation carefully considered a variety of protocols, including the appropriate choice of the force field, rigorous standardization reflecting the experimental conditions, sampling algorithm, anisotropic environment, and collective variables, to accurately describe GpA dimerization via molecular dynamics-based approaches. Specifically, two strategies were explored: (i) an unrestrained potential mean force (PMF) calculation, which merely enhances sampling along the separation of the two binding partners without any restraint, and (ii) a so-called "geometrical route", whereby the α-helices are progressively separated with imposed restraints on their orientational, positional, and conformational degrees of freedom to accelerate convergence. Our simulations reveal that the simplified, unrestrained PMF approach is inadequate for the description of GpA dimerization. Instead, the geometrical route, tailored specifically to GpA in a membrane environment, yields excellent agreement with experimental data within a reasonable computational time. A dimerization free energy of -10.7 kcal/mol is obtained, in fairly good agreement with available experimental data. The geometrical route further helps elucidate how environmental forces drive association before helical interactions stabilize it. Our simulations also brought to light a distinct, long-lived spatial arrangement that potentially serves as an intermediate state during dimer formation. The methodological advances in the generalized geometrical route provide a powerful tool for accurate and efficient binding-affinity calculations of intricate TM protein complexes in inhomogeneous environments.

Variety of forms of phytoliths of Kulunda soils and their phytocenotic affiliation

Phytoliths are an important component of soil and vegetation cover. Thanks to phytolith analysis, it is possible to identify vegetation cover after a long time. There is practically no information about the transition of amorphous silica in the form of phytoliths from plant mass to soil. This very important stage in the formation of the soil phytolith spectrum was considered in the works of N. K. Kiseleva. When studying the phytolith spectra of dominant grasses and sedges, she calculated the coefficient of their participation for the Mongolian steppes, and further she proposed the concept of “phytolith spectrum" In this work, we made an attempt to assess the correlation of the set of phytolith forms and their ratio in the upper soil layer with the modern composition of vegetation. For this purpose, the phytolith spectra of soils and vegetation of three ecosystems were analyzed, and the phytolith spectra of modern soils were compared. We also applied the approach of Nina Kiseleva and the results we obtained of taxonomic diagnosis of plant species based on the forms of their phytoliths. The research was carried out on the territory of the North Kulunda lacustrine-alluvial plain. The phytolith complex of the surface layer of soils of the forb-fescue with wormwood steppe is characterized by the predominance of two groups of phytoliths: truncated cone-shaped (RONDEL) phytoliths and trapezoidal wavy plates (CRENATE). In the soils of the bushy feather-grass-forb steppe and solonetzic steppe with a cereal-licorice community, trapezoidal polylobed plates (CRENATE) and bilobed particles (BILOBATE) are added to them. Other indicator forms are presented in small quantities. Calculation of the soil phytolith complex allows one to diagnose the coenotic composition of cereals of the phytolith spectrum.

Crystal structure, Hirshfeld surface analysis and energy framework calculations of different metal complexes of a biphenol-based ligand: Role of solvent and transition metal ion

A new Pd(II) complex of the previously reported ligand N,N′-bis[(2,2′-dihydroxybiphen-3-yl)methyl]-N,N′-dimethylethylenediamine (L) was obtained from N,N-dimethylformamide/water. The roles in the solid state assembly of solvent molecules and molecular conformation were studied by comparing six complexes of L containing different metal centers (Ni(II), Cd(II), Cu(II), Pd(II)). Hirshfeld surface analysis, 2D fingerprint plots and energy frameworks calculations were used to investigate the intermolecular interactions within the crystal packings. Pd(II) and Ni(II) complexes arrange to form ribbons, while Cd(II) and Cu(II) complexes form 3D networks. Interactions between complexes and solvent molecules in the previously reported Pd(II) complex are replaced by complex-complex interactions in the new Pd(II) complex, while butanol and methanol are interchangeable in the interactions within the Ni(II) complexes. The present study suggested that the solid state assembly of these systems is mainly driven by the molecular conformation, that depends in turn by the metal ion involved, while the solvent only plays a minor role.

Evaluation and Analysis of Heuristic Intelligent Optimization Algorithms for PSO, WDO, GWO and OOBO

In order to comprehensively evaluate and analyze the effectiveness of various heuristic intelligent optimization algorithms, this research employed particle swarm optimization, wind driven optimization, grey wolf optimization, and one-to-one-based optimizer as the basis. It applied 22 benchmark test functions to conduct a comparison and analysis of performance for these algorithms, considering descriptive statistics such as convergence speed, accuracy, and stability. Additionally, time and space complexity calculations were employed, alongside the nonparametric Friedman test, to further assess the algorithms. Furthermore, an investigation into the impact of control parameters on the algorithms’ output was conducted to compare and analyze the test results under different algorithms. The experimental findings demonstrate the efficacy of the aforementioned approaches in comprehensively analyzing and comparing the performance on different types of intelligent optimization algorithms. These results illustrate that algorithm performance can vary across different test functions. The one-to-one-based optimizer algorithm exhibited superior accuracy, stability, and relatively lower complexity.

The asymptotic distribution of the permutation entropy.

Ordinal patterns serve as a robust symbolic transformation technique, enabling the unveiling of latent dynamics within time series data. This methodology involves constructing histograms of patterns, followed by the calculation of both entropy and statistical complexity-an avenue yet to be fully understood in terms of its statistical properties. While asymptotic results can be derived by assuming a multinomial distribution for histogram proportions, the challenge emerges from the non-independence present in the sequence of ordinal patterns. Consequently, the direct application of the multinomial assumption is questionable. This study focuses on the computation of the asymptotic distribution of permutation entropy, considering the inherent patterns' correlation structure. Furthermore, the research delves into a comparative analysis, pitting this distribution against the entropy derived from a multinomial law. We present simulation algorithms for sampling time series with prescribed histograms of patterns and transition probabilities between them. Through this analysis, we better understand the intricacies of ordinal patterns and their statistical attributes.

Alkynylphosphonium Pt(II) Complexes: Synthesis, Characterization, and Features of Photophysical Properties in Solution and in the Solid State.

A series of heteroleptic bis-alkynyl-diimine mononuclear Pt(II) complexes with alkynylphosphonium and di-tert-butyl-2,2'-bipyridine (dtbpy) ligands have been prepared and characterized by spectroscopic methods and single-crystal XRD. The Pt(II) complexes obtained in the present study demonstrate triplet emission in solution, which originates from 3MLCT/3LC states where the nature of the π-conjugated linker in the alkynylphosphonium ligand manages the contributions of each transition, and this conclusion is supported by DFT calculations. Additionally, the presence of the phosphonium group connected to alkynyl through the π-conjugated linker enhances nonlinear optical properties of the Pt(II) complexes increasing two-photon absorption cross section up to 400 GM. In the solid state, the Pt(II) complexes demonstrate emission that is attributed to 3MMLCT transitions due to the presence of Pt-Pt metallophilic interactions, and the reversible assembly and disassembly of these interactions by grinding and solvent treatment are responsible for the mechanochromic luminescence. It has been experimentally shown that stimuli-responsive emission of the Pt(II) complexes is the result of a "monomer/dimer" transformation; this conclusion is confirmed by DFT calculations for discrete complexes and different dimers with or without Pt-Pt interactions.

Standard Binding Free-Energy Calculations: How Far Are We from Automation?

Recent success stories suggest that in silico protein-ligand binding free-energy calculations are approaching chemical accuracy. However, their widespread application remains limited by the extensive human intervention required, posing challenges for the neophyte. As such, it is critical to develop automated workflows for estimating protein-ligand binding affinities with minimum personal involvement. Key human efforts include setting up and tuning enhanced-sampling or alchemical-transformation algorithms as a preamble to computational binding free-energy estimations. Additionally, preparing input files, bookkeeping, and postprocessing represent nontrivial tasks. In this Perspective, we discuss recent progress in automating standard binding free-energy calculations, featuring the development of adaptive or parameter-free algorithms, standardization of binding free-energy calculation workflows, and the implementation of user-friendly software. We also assess the current state of automated standard binding free-energy calculations and evaluate the limitations of existing methods. Last, we outline the requirements for future algorithms and workflows to facilitate automated free-energy calculations for diverse protein-ligand complexes.

Qualitative and quantitative contributions of intermolecular interactions, quantum chemical calculation, biological activity and visible-light driven photo catalysts studies of nickel complex of 4-amino-N-(5-methyl-1,3,4-thiadiazol-2-yl)benzenesulfonamide

This study reports the successful synthesis and characterization of a nickel complex of the sulfamethizole (smtz) ligand. The complex was characterized using 1H NMR and FT-IR spectroscopic analyses. The synthesized complex exhibited promising properties as a biological and visible light-driven photocatalyst. Under visible light radiation, it displayed remarkable photo-degradation capabilities, achieving a degradation efficiency of 91.2% within 80 min against a solution of methylene blue (MB) with a concentration of 10 PPM in 100 mL. To understand the complex's biological response, viscosity measurements were conducted to investigate its mode of binding with CT-DNA. The results demonstrated that the nickel complex exhibited stronger inhibitory activity and lower cytotoxicity compared to the smtz ligand, as evidenced by cytotoxic analysis and minimum inhibitory concentration (MIC) data against a range of gram-positive and gram-negative pathogens. Furthermore, the crystal structure of the complex was determined through single-crystal X-ray diffraction analysis, revealing its crystallization in the triclinic space group P-1. The asymmetric part of the unit cell consisted of a Ni0.5 metal atom, one -Picoline solvent molecule, one smtz ligand, and one coordinated water molecule. To gain further insights into the complex's properties, Hirshfeld surfaces (HS) and a 3D energy framework approach were utilized to visualize its active and inactive surfaces. The analysis indicated that the dispersion energy contribution in molecular packing was significantly greater than that of electrostatic energy. Additionally, calculations of the HOMO-LUMO energy and other quantum chemical parameters were performed to understand the molecule's stability. Overall, the synthesized nickel complex of the sulfamethizole ligand exhibited remarkable photocatalytic properties, strong inhibitory activity against pathogens, and a stable crystal structure. These findings contribute to the understanding of the complex's potential applications in photocatalysis and biomedical research.

DFT calculations of copper complexes mimicking superoxide dismutase and docking studies and molecular dynamics of the transition metal complex binding to serum albumin

Superoxide dismutase (SOD) is a metalloenzyme whose antioxidant activity is mimicked by some transition metal complexes, and such ability can be added in proteins such as the bovine serum albumin (BSA), creating a hybrid protein. In this work, density functional theory (DFT) calculations of three Cu(II)-complexes of general formula [CuL2phen] (phen = phenanthroline; C1, L = mefenamate; C2, L = tolfenamate; C3, L = flufenamate) with SOD-like activity, and docking and molecular dynamics (MD) simulations of these complexes with the BSA were performed. The DFT calculations revealed that the complex reduction involves Cu(II) → Cu(I) reduction, the theoretical electron affinity (EA) correlated with the SOD-like activity (IC50), and the contribution of the phenanthroline ligand and the metal in LUMO it’s related with the complex-protein interaction (KVS). The docking and MD simulations revealed the binding site of the complexes in BSA and the residues involved in the binding. The stability of the Cu(II) and Cu(I) forms of the complexes in the site indicated that the catalysis promoted by these complexes occurs in the same region of the BSA and that their mimetic activity can be incorporated into BSA, creating a hybrid protein (BSA with SOD activity) Communicated by Ramaswamy H. Sarma

Landscape complexity beyond invariance and the elastic manifold

AbstractThis paper characterizes the annealed, topological complexity (both of total critical points and of local minima) of the elastic manifold. This classical model of a disordered elastic system captures point configurations with self‐interactions in a random medium. We establish the simple versus glassy phase diagram in the model parameters, with these phases separated by a physical boundary known as the Larkin mass, confirming formulas of Fyodorov and Le Doussal. One essential, dynamical, step of the proof also applies to a general signal‐to‐noise model of soft spins in an anisotropic well, for which we prove a negative‐second‐moment threshold distinguishing positive from zero complexity. A universal near‐critical behavior appears within this phase portrait, namely quadratic near‐critical vanishing of the complexity of total critical points, and cubic near‐critical vanishing of the complexity of local minima. These two models serve as a paradigm of complexity calculations for Gaussian landscapes exhibiting few distributional symmetries, that is, beyond the invariant setting. The two main inputs for the proof are determinant asymptotics for non‐invariant random matrices from our companion paper (Ben Arous, Bourgade, McKenna 2022), and the atypical convexity and integrability of the limiting variational problems.

Synthesis, Spectroscopic Characterization and DFT Calculations of a Novel Lanthanum Complex of Ferrocenyl Dithiophosphonate

Synthesis, Spectroscopic Characterization and DFT Calculations of a Novel Lanthanum Complex of Ferrocenyl Dithiophosphonate

Europium(III) and gallic acid ligand coordination compounds: synthesis, characterization, photophysical processes, and optimization of luminescent properties

We obtained EuIII, GdIII, and GdIII doped with EuIII (1 at.% and 5 at.%) complexes with the ligand derived from 3,4,5-trihydroxybenzoic acid (H4Gal). Synthetic routes are proposed from acetate and chloride solutions of the trivalent lanthanides. We demonstrated the decomposition of the ligands 3,4,5-trihydroxybenzoate (H3Gal ≡ L–) and 3-hydroxo-4,5-dihydroxybenzoate (H2Gal2– ≡ L’2–) in an acetic solution medium. [LnLL’(H2O)2] complexes are obtained in a metal chloride solution medium. We studied the complexes in the solid state. We described the photophysical processes in the complexes, and they resulted in an energy diagram of the EuIII compounds in which the position of the states related to the LMCT transition are intermediate to the ligand's singlet (S1) and triplet (T1) states. We obtained the position of the triplet state (T1) from the luminescence of the GdIII complex. We performed the calculations of the EuIII complex's electronic structure using the Lumpac software to confirm the propositions obtained through experiments. The proposition is that the excitation in the LMCT state rapidly populates the T1 state, and the L–L’2–→EuIII back energy transfer may occur. One of the possible disadvantages of the complexes is the enormous non-radioactive deactivation due to the oscillators (OH) and (CH). The EuIII characteristic luminescence is of little intensity. We obtained GdIII compounds doped with EuIII at 1.0 and 5.0 at.% to optimize luminescent properties. We obtained the emission and excitation spectra of the complexes at 77 and 17 K, showing ligands' phosphorescence superimposed on the characteristic emissions 5D0 →7FJ (J = 0–4) of the EuIII ion.

5-(2-pyridyl)tetrabenzoporphyrin and its complexes with zinc, cobalt, copper and iron. synthesis, spectral, electrochemical and electrocatalytic properties

The interaction of phthalimide with 2-picoline in the presence of zinc oxide synthesized 3-(pyridin-2-ylmethylene)isoindolin-1-one. Heating its mixture with an excess of phthalimide and zinc acetate leads to the formation of zinc 5-(2-pyridyl)tetrabenzoporphyrinate, which, upon treatment with acid, is converted to 5-(2-pyridyl) tetrabenzoporphyrin. The latter, when interacting with cobalt(II), copper(II), and iron(III) chlorides in DMF, forms the corresponding metal complexes. The composition and structure of the obtained compounds were confirmed by mass spectrometry, vibrational, 1H NMR, and electron spectroscopy. The results of quantum-chemical calculations of complexes by the DFT method are presented. A correlation is established between the energy gap between the frontier orbitals and the positions of the first bands in the electronic absorption spectra. All the synthesized tetrabenzoporphyrins exhibit catalytic activity in the electroreduction of oxygen, the highest activity being exhibited by cobalt and copper complexes.

Synthesis, structure of luminescence complexes and metalopolymers of Dy(III) and influence of the nature of substitutes on their emission

The new complexes of Dy (III) other β-diketones containing unsaturated, alkyl- and aryl- substituents were obtainted. Their heteroligand complexes with phenanthroline were synthesized. Quantum-chemical calculations of ligand molecules and metal complexes were performed. The main energy characteristics of ligand molecules were calculated: enthalpy of formation, total energy of the molecule and bond lengths, electronic population parameters of ligands. Metal polymers based on synthesized complexes were obtained by the method of radical polymerization. The composition and structure of synthesized complexes and metal polymers are established. It is shown that during polymerization the coordination environment of the central ion remains unchanged. The spectral-luminescent characteristics of the synthesized compounds were studied. The peculiarities of the influence of substituents in the diketonate fragment on the luminescent properties of metal complexes have been established. It is shown that the emission intensity of powdered samples depends on their morphology and dispersion.