Energy Decomposition Analysis Research Articles

Conformational Preference of Lithium Polysulfide Clusters Li2Sx (x = 4-8) in Lithium-Sulfur Batteries.

Structures are of fundamental importance for diverse studies of lithium polysulfide clusters, which govern the performance of lithium-sulfur batteries. The ring-like geometries were regarded as the most stable structures, but their physical origin remains elusive. In this work, we systematically explored the minimal structures of Li2Sx (x = 4-8) clusters to uncover the driving force for their conformational preferences. All low-lying isomers were generated by performing global searches using the ABCluster program, and the ionic nature of the Li···S interactions was evidenced with the energy decomposition analysis based on the block-localized wave function (BLW-ED) approach and further confirmed with the quantum theory of atoms in molecule (QTAIM). By analysis of the contributions of various energy components to the relative stability with the references of the lowest-lying isomers, the controlling factor for isomer preferences was found to be the polarization interaction. Notably, although the electrostatic interaction dominates the binding energies, it contributes favorably to the relative stabilities of most isomers. The Li+···Li+ distance is identified as the key geometrical parameter that correlates with the strength of the polarization of the Sx2- fragment imposed by the Li+ cations. Further BLW-ED analyses reveal that the cooperativity of the Li+ cations primarily determines the relative strength of the polarization.

Directionality of Halogen-Bonds: Insights from 2D Energy Decomposition Analysis.

Halogen bonds are typically observed to have a linear arrangement with a 180° angle between the nucleophile and the halogen bond acceptor X-R. This linearity is commonly explained using the σ-hole model, although there have been alternative explanations involving exchange repulsion forces. We employ two-dimensional Distortion/Interaction and Energy Decomposition Analysis to examine the archetypal H3 N⋯X2 halogen bond systems. Our results indicate that although halogen bonds are predominantly electrostatic, their directionality is largely due to decreased Pauli repulsion in linear configurations as opposed to angled ones in the I2 and Br2 systems. As we move to the smaller halogens, Cl2 and F2 , the influence of Pauli repulsion diminishes, and the energy surface is shaped by orbital interactions and electrostatic forces. These results support the role of exchange repulsion forces in influencing the directionality of strong halogen bonds. Additionally, we demonstrate that the 2D Energy Decomposition Analysis is a useful tool for enhancing our understanding of the nature of potential energy surfaces in noncovalent interactions.

Matrix-isolation FTIR spectroscopic study and quantum chemical calculations of 1:1 adduct of CHCl3 and C2H5OH in N2 matrix

[▪-▪] mixture is a common binary solvent used in industries, organic synthesis, lipid extraction, drug extraction, etc. The purpose of this study is to have a molecular level understanding of the interaction of ▪ with ▪. The experiments have been carried out in low temperature ▪ matrix using Fourier Transform Infrared spectroscopy. Electronic structure calculations have been performed to identify the possible binding motifs between ▪ and ▪. Three minima have been obtained on the dimer potential energy surface stabilised by ▪ and ▪ hydrogen bond, and ▪ halogen bond interactions. Formation of more than one complexes have been confirmed using the experimental and simulated IR spectra. Energy decomposition analysis and Natural bond orbital analysis have been performed to understand the nature of interaction and the driving force for complexation. This is one of the first reports where separate complexes have been identified between ▪ and anti and gauche conformers of ▪ in the low temperature matrix.

Catalyst-Controlled Intermolecular Homobenzylic C(sp3)-H Amination for the Synthesis of β-Arylethylamines.

The combination of a tailored sulfamate with a C4-symmetrical rhodium(II) tetracarboxylate allows to uncover a selective intermolecular amination of unactivated homobenzylic C(sp3)-H bonds. The reaction has a broad scope (>30 examples) and proceeds with a high level of regioselectivity with homobenzylic/benzylic ratio of up to 35:1, thereby providing a direct access to β-arylethylamines that are of utmost interest in medicinal chemistry. Computational investigations evidenced a concerted mechanism, involving an asynchronous transition state. Based on a combined activation strain model and energy decomposition analysis, the regioselectivity of the reaction was found to rely mainly on the degree of orbital interaction between the [Rh2]-nitrene and the C-H bond. The latter is facilitated at the homobenzylic position due to the establishment of specific noncovalent interactions within the catalytic pocket.

In Silico Analysis of the Aromaticity of Some Carbo-Metallabenzenes and Carbo-Dimetallabenzenes (Carbo-mers Proposed from Metallabenzenes).

In the current work, we introduce a novel class of molecules termed carbo-metallabenzenes, and their aromaticity has been comprehensively analyzed. The molecules were strategically designed with the insertion of acetylene (C≡C or C2) units in some selected metallabenzenes. Furthermore, if a second metallic unit is inserted (replacing a sp2 carbon) in the carbo-metallabenzenes rings, a new family of carbo-mers is generated, and this second group has been named as carbo-dimetallabenzenes. The primary objective of this work is to ascertain, through various methodologies, whether these newly proposed molecules retain the aromatic characteristics observed in carbo-benzene. The methodologies employed for bond analysis and aromaticity exploration include the analysis of the molecular orbitals, energy decomposition analysis, electron density of delocalized bonds, magnetically induced current density, and the induced magnetic field (Bind). This study sheds light on that the insertion of the metallic centers reduces the electronic delocalization and their aromaticity is, in some cases, comparable with the electronic delocalization of the inorganic iminobora-borazine and also provides valuable insights into their electronic structure through a multifaceted analysis.

Size Matters: Computational Insights into the Crowning of Noble Gas Trioxides.

In pursuit of enhancing the stability of the highly explosive and shock-sensitive compound XeO3, we performed quantum chemical calculations to investigate its possible complexation with electron-rich crown ethers, including 9-crown-3, 12-crown-4, 15-crown-5, 18-crown-6, and 21-crown-7, as well as their thio analogues. Furthermore, we expanded our study to other noble gas trioxides (NgO3), namely, KrO3 and ArO3. The basis set superposition error (BSSE) corrected interaction energies for these adducts range from -13.0 kcal/mol to -48.2 kcal/mol, which is notably high for σ-hole-mediated noncovalent interactions. The formation of these adducts was observed to be more favorable with the increase in the ring size of the crowns and less favorable while going from XeO3 to ArO3. A comprehensive analysis by various computational tools such as the mapping of the electrostatic potential (ESP), Wiberg bond indices (WBIs), Bader's theory of atoms-in-molecules (AIM), natural bond orbital (NBO) analysis, noncovalent interaction (NCI) plots, and energy decomposition analysis (EDA) revealed that the C-H···O interactions, as well as dispersion interactions, play a pivotal role in stabilizing adducts involving larger crowns. A noteworthy outcome of our study is the revelation of a coordination number of 9 for xenon in the complex formed between XeO3 and the thio analogue of 18-crown-6, which is higher than the largest number reported to date.

Enhancement of gas adsorption on transition metal ion-modified graphene using DFT calculations.

Graphene-based nanomaterial was widely used in gas sensors, detection, and separation. However, weak adsorption and low selectivity of the pristine graphene used for gas sensors are major problems. Here, using density functional theory (DFT) calculations, we reported the significant increase of four gas molecules (N2, CO2, C2H2, and C2H4) adsorption on the transition metal ion (Fe3+, Co2+, Ni2+)-modified graphene complex (Fe3+/Co2+/Ni2+-G) comparing to be absorbed on the pristine graphene (G). Moreover, the Co2+-G is suitable for the selective separation of C2H4/C2H2 due to the larger adsorption energy difference (8.5kcal/mol) between them. The addition of transition metal ions also decreased the HOMO-LUMO gap of the systems, which benefits the enhancement of electrical conductivity. This suggests that the transition metal ion-modified graphene can be used to distinguish the different gas molecule's adsorption, facilitating the design of graphene-based gas sensors and selective separation. All the density functional theory (DFT) calculations were performed by B3LYP with the GD3 dispersion method using Gaussian 16 software. The basis set 6-31G(d) was used for C, H, O, and N atoms, and Lanl2DZ was used for transition metal ions (Fe3+, Co2+, Ni2+). The DOS analysis and energy decomposition analysis were performed using the Multiwfn program.

Exploring Unconventional σ-Hole Interactions: Computational Insights into the Interaction of XeO3 with Non-Aromatic Coordinating Solvents.

In order to control the explosiveness and shock sensitivity of XeO3 , we have investigated its plausible interaction with various non-aromatic coordinating solvents, serving as potential Lewis base donors, through density functional theory (DFT) calculations. Out of twenty six such solvents, the top ten were thus identified and then thoroughly examined by employing various computational tools such as the mapping of the electrostatic potential surface (MESP), Wiberg bond indices (WBIs), non-covalent interaction (NCI) plots, Bader's theory of atoms-in-molecules (AIM), natural bond orbital (NBO) analysis, and the energy decomposition analysis (EDA). The amphoteric nature of XeO3 was also explored by investigating the extent of back donation from the lone pair of Xe to the antibonding orbital of the donating atom/group of the solvent molecules. The C-H…O interactions were also found to be a contributing factor in the stabilization of these adducts. Although these aerogen-bonding interactions were found to be predominantly electrostatic, significant contributions from the orbital contributions, as well as dispersion interactions, were observed. The top three non-aromatic solvents (among the twenty six studied) which form the strongest adducts with XeO3 are proposed to be hexamethylphosphoramide (HMPA), N,N'-dimethylpropyleneurea (DMPU) and tetramethylethylenediamine (TMEDA).

A Deeper Insight into the Supramolecular Activation of Oxidative Addition Reactions Involving Pincer-Rhodium(I) Complexes.

The factors governing the acceleration of the oxidative addition of methyl iodide to pincer rhodium(I)-complexes induced by coronene have been computationally explored in detail using quantum chemical methods. Both the parent reaction and the coronene-mediated process proceed via a stepwise SN2-type mechanism. It is found that the acceleration of the process derives from the formation of an initial supramolecular complex, mainly stabilized by electrostatic and π-π interactions, which significantly increases the electron richness of the complex. The impact of this effect on the reaction barrier has been quantitatively analyzed by applying the activation strain model in combination with the energy decomposition analysis method. In addition, the influence of other polycyclic aromatic hydrocarbons on the oxidative reaction has been also considered.

Observation of a super-tetrahedral cluster of acetonitrile-solvated dodecaborate dianion via dihydrogen bonding

We launched a combined negative ion photoelectron spectroscopy and multiscale theoretical investigation on the geometric and electronic structures of a series of acetonitrile-solvated dodecaborate clusters, i.e., B12H122−·nCH3CN (n = 1–4). The electron binding energies of B12H122−·nCH3CN are observed to increase with cluster size, suggesting their enhanced electronic stability. B3LYP-D3(BJ)/ma-def2-TZVP geometry optimizations indicate each acetonitrile molecule binds to B12H122− via a threefold dihydrogen bond (DHB) B3–H3 ⁝⁝⁝ H3C–CN unit, in which three adjacent nucleophilic H atoms in B12H122− interact with the three methyl hydrogens of acetonitrile. The structural evolution from n = 1 to 4 can be rationalized by the surface charge redistributions through the restrained electrostatic potential analysis. Notably, a super-tetrahedral cluster of B12H122− solvated by four acetonitrile molecules with 12 DHBs is observed. The post-Hartree–Fock domain-based local pair natural orbital- coupled cluster singles, doubles, and perturbative triples [DLPNO-CCSD(T)] calculated vertical detachment energies agree well with the experimental measurements, confirming the identified isomers as the most stable ones. Furthermore, the nature and strength of the intermolecular interactions between B12H122− and CH3CN are revealed by the quantum theory of atoms-in-molecules and the energy decomposition analysis. Ab initio molecular dynamics simulations are conducted at various temperatures to reveal the great kinetic and thermodynamic stabilities of the selected B12H122−·CH3CN cluster. The binding motif in B12H122−·CH3CN is largely retained for the whole halogenated series B12X122−·CH3CN (X = F–I). This study provides a molecular-level understanding of structural evolution for acetonitrile-solvated dodecaborate clusters and a fresh view by examining acetonitrile as a real hydrogen bond (HB) donor to form strong HB interactions.

Introduction of 5-membered boron-oxygen-heterocyclic carbene and its Si and Ge homologs and the M–L bonding analysis in their complexes with coinage metals: A theoretical study

Replacing an oxygen atom with one of the boron atoms in a 5-membered B-Heterocyclic carbene and its Si and Ge congeners (BHEs; E = C, Si, Ge) creates Boron-Oxygen-Heterocyclic divalents (BOHEs) which may have potential uses as organometallic ligands. In addition to a survey on their singlet–triplet energy gap (ΔET-S) for the stability concerns, the nature of the E–M bonds in XBOHE–MCl complexes (M = CuI, AgI, AuI; E = C, Si, Ge; X = F, Cl, Br) is theoretically investigated using the natural bond orbital (NBO), energy decomposition analysis (EDA), and extended transition state natural orbital for chemical valence (ETS-NOCV) analysis. The outcomes show interesting stabilities of singlet/triplet configurations in carbenes, silylenes, and germylenes. Also, the results exhibit that the E–M bonds in the complexes have a higher electrostatic character.

Computational study on the characteristics of the complexes resulting from the interaction of carbonyl selenide and hypohalous acids

This study computationally investigates the properties and competition of complexes formed by the interaction between hypohalous acids (HOX, where X = F, Cl, Br, and I) and carbonyl selenide (COSe) at the MP2/aug-cc-pVTZ computational level. Three distinct groups of complexes were obtained. The first group, consisting of complexes with a cyclic structure (HB-TB), exhibited the highest stability. remaining two groups formed less stable linear structures with different characteristics (ChB and XB). In the first group, the electronegativity of the halogen atom significantly influenced the stability of the complexes. Conversely, the stability of complexes in groups II and III was primarily determined by the acid and base strengths of the interacting monomers. To comprehensively evaluate the obtained results, various analyses were employed, including Molecular electrostatic potential (MEP), geometry Optimization, Spectroscopic, Interaction energy (SE), Natural bond orbital (NBO) analysis, Atoms in molecules (AIM) analysis, Non-covalent interaction (NCI) index, Energy decomposition analysis (EDA), and Electron density difference(EDD) analysis.

3-styrylcoumarin scaffold-based derivatives as a new approach for leishmaniasis intervention: biological and molecular modeling studies

Seven 3-styrylcoumarins were tested for antileishmanial activity against Leishmania (Viannia) panamensis amastigotes. Cytotoxic activity was also evaluated against mammalian U-937 cells. The 3-methoxy-4-hydroxy coumarin derivative 6 was the most active with an IC50 of 40.5 µM, and did not reveal any conspicuous toxicity toward mammalian U-937 cells. Therefore, it may have potential to be considered as candidate for antileishmanial drug development. Further, among several druggable Leishmania targets, molecular docking studies revealed that compound 6 had docking preference by the N-myristoyltransferase (Lp-NMT) of Leishmania panamensis, showing a higher docking score of − 10.1 kcal mol−1 than positive controls and making this protein as a presumably druggable target for this compound. On the other hand, molecular dynamics simulations affirm the docking hypothesis, showing a conformational stability of the 6/Lp-NMT complex throughout 100 ns simulation. Moreover, the molecular mechanics/Poisson–Boltzmann surface area method also support the docking findings, revealing a total free energy of binding of − 47.26 ± 0.08 kcal mol−1, and identifying through energy decomposition analysis that those key aminoacids are contributing strongly to ligand binding. Finally, an optimal pharmacokinetic profile was also estimated for 6. Altogether, coumarin 6 could be addressed as starting point for further pharmacological studies concerning the therapeutic leishmaniasis intervention.Graphical abstract

Metal Influence on Cyaphide-Azide 1,3-Dipolar Cycloaddition Reactions: Aromaticity and Activation Strain.

The factors governing 1,3-dipolar cycloaddition reactions involving C≡P-containing compounds are computationally explored in detail using quantum chemical tools. To this end, the parent process involving tBuN3 and tBuCP is analyzed and compared to the analogous reaction involving organometallic cyaphide complexes (metal=Au, Pt, Ge, Mg), in order to understand the role of the metal fragment in such transformations. It is found that while the metal fragment does not significantly influence the aromaticity of the corresponding concerted transition states or the regioselectivity of the transformation, it may modify the reactivity of the cyaphide complexes (i. e. Ge and Mg cyaphide complexes are comparatively more reactive). The computed reactivity trends and the factors behind the regioselectivity of the cycloaddition reaction are quantitatively analyzed with the help of the activation strain model in combination with the energy decomposition analysis method.

Theoretical study on formation mechanism of acetic acid associating configurations and their distributions under saturated conditions.

The vapor-liquid equilibrium (VLE) properties of acetic acid systems generally behave strong non-ideality due to the associating interaction among acetic acid molecules. Theoretical study of the associating mechanism will provide guidance for the VLE property prediction, which is crucial for the designing on the separation process of the acetic acid systems. In this work, the association conformers and their distribution on acetic acid molecules in saturated gas and liquid phase were firstly studied. The proportions of the acetic acid monomer and multimers were obtained, which will contribute to the foundation for the vapor-liquid equilibrium simulations. The association mechanism on acetic acid molecules was then investigated by comparing among the structures and non-bonded interaction energies of different dimers. The structure of the cyclic dimer containing two OC-HO hydrogen bonds, may be found probably when acetic acid molecules approached. Electronic properties of different acetic acid dimers showed that the electrons around carbonyl oxygen atoms were deflected by the attraction of hydrogen atoms in the other molecule, which polarized the acetic acid molecules when the hydrogen bonds between acetic acid molecules were formed, providing theoretical basis for the polarized acetic acid molecular model. In this work, the molecular dynamics (MD) simulations and DFT calculations were conducted through the software GROMACS and Gaussian 09, respectively. For the MD simulations, the OPLS-AA force field was used as the atomic force field, with the cubic simulation cells constructed by Packmol program. For the DFT calculations, the M06-2X functional was employed for the optimization of the associating structures with the 6-311G** basis sets. Hydrogen bonding energies of dimers were corrected for the basis set superposition error (BSSE) and the deformation energies of monomers. Furthermore, the energy decomposition analysis was conducted at DFT/M06-2X/def-tzp level by the ADF software, and the wave function analysis was conducted by the Multiwfn software including the atom in molecule (AIM) topology analysis, the electronic potential analysis, and the electron density difference analysis.

Mono(Lewis Base)-Stabilized Gallium Iodide: An Unexplored Class of Promising Ligands.

Quantum-chemical (DFT) calculations on hitherto unknown base(carbene)-stabilized gallium monoiodides (LB→GaI) suggest that these systems feature one lone pair of electrons and a formally vacant p-orbital - both centered at the central gallium atom - and exhibit metallomimetic behavior. The calculated reaction free energies as well as bond dissociation energies suggest that these LB→GaI systems are capable of forming stable donor-acceptor complexes with group 13 trichlorides. Examination of the ligand exchange reactions with iron and nickel complexes indicates their potential use as ligands in transition metal chemistry. In addition, it is found that the title compounds are also able to activate various enthalpically robust bonds. Further, a detailed mechanistic investigation of these small molecule activation processes reveals the non-innocent behavior of the carbene (base) moiety attached to the GaI fragment, thereby indicating the cooperative nature of these bond activation processes. The energy decomposition analysis (EDA) and activation strain model (ASM) of reactivity were also employed to quantitatively understand and rationalize the different activation processes.

Solvent role in molecular structure level, structural and topology investigations, molecular docking and antimicrobial activity studies on sulpha drug derivative

The Schiff base (5FSATH) was synthesized and characterized by different experimental techniques. In the context of local energy decomposition analysis (LED), the binding energy of 5FSATH-water interaction is determined to be -15.63 kcal/mol, while the bond distance between the two objects is measured to be 1.9781 A°. The absorption spectrum was recorded using different solvents like DMSO, water, and chloroform. The experimental absorption spectrum wavelengths 206, 220, and 300 nm, were recorded from DMSO solvent. In the emission (fluorescence) spectrum we observed three different wavelengths such as 352, 510, and 609 nm. For the calculated NMR spectrum, used the standard GIAO method and DMSO as the solvent. The HOMO-LUMO analysis indicates the charge transfer within the molecule, it is calculated by different solvents. NBO confirms the synthesized compound stability, hyper conjugative interaction, and charge delocalization. To test for antibacterial and antifungal activity, an agar disc well diffusion method is utilized. Synthesized compound tested against Escherichia coli, Candida albicans, Staphylococcus aureus, and Streptococcus pneumoniae microorganisms. Amoxicillin was used as the reference drug for testing antibacterial and antifungal activity. According to the findings of the antimicrobial activity, the result of the molecular docking experiment showed that the compound 5FSATH had an extremely high binding affinity score.

A facile synthesis, characterization, DFT, ADMET and in-silico molecular docking analysis of novel 4-ethyl acridine-1,3,9 (2,4,10H)-trione

A novel synthetic reaction was employed to produce an acridine derivative of 4-ethyl acridine-1,3,9 (2,4,10H)-trione. The structural characterizations of the synthesized compound were confirmed through FT-IR, NMR 1H,13C, and GC-Mass spectral data. Furthermore, the DFT approaches were performed to the vibrational wavenumbers obtained through simulation with experimental wave numbers. The Vibrational Energy Distribution Analysis (VEDA) software is employed in FT-IR wave number for conducting potential energy decomposition (PED) analysis. DFT calculations were also applied to optimize the structural parameters and investigate Frontier molecular orbitals (FMOs), molecular electrostatic potentials, RDG studies, and global chemical reactivity descriptors, Natural bond orbital analysis and Non-linear optical properties were obtained for the title compound using the DFT method. Molecular docking studies were conducted to explore the binding mode mechanism of title compound and were evaluated for cancer-related proteins, specifically 4y72. Also, the synthesised compound was evaluated for Drug-likeness, and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties indicating favourable pharmacokinetic profiles with no observed signs of toxicity.

T-Shaped Palladium and Platinum {MNO}10 Nitrosyl Complexes.

The synthesis and characterization of a homologous series of T-shaped {MNO}10 nitrosyl complexes of the form [M(PR3)2(NO)]+ (M = Pd, Pt; R = tBu, Ad) are reported. These diamagnetic nitrosyls are obtained from monovalent or zerovalent precursors by treatment with NO and NO+, respectively, and are notable for distinctly bent M-NO angles of ∼123° in the solid state. Adoption of this coordination mode in solution is also supported by the analysis of isotopically enriched samples by 15N NMR spectroscopy. Effective oxidation states of M0/NO+ are calculated, and metal-nitrosyl bonding has been interrogated using DFT-based energy decomposition analysis techniques. While a linear nitrosyl coordination mode was found to be electronically preferred, the M-NO and P-M-P angles are inversely correlated to the extent that binding in this manner is prevented by steric repulsion between the bulky ancillary phosphine ligands.

The Pivotal Distinction between Antagonists' and Agonists' Binding into Dopamine D4 Receptor-MD and FMO/PIEDA Studies.

The dopamine D4 receptor (D4R) is a promising therapeutic target in widespread diseases, and the search for novel agonists and antagonists appears to be clinically relevant. The mechanism of binding to the receptor (R) for antagonists and agonists varies. In the present study, we conducted an in-depth computational study, teasing out key similarities and differences in binding modes, complex dynamics, and binding energies for D4R agonists and antagonists. The dynamic network method was applied to investigate the communication paths between the ligand (L) and G-protein binding site (GBS) of human D4R. Finally, the fragment molecular orbitals with pair interaction energy decomposition analysis (FMO/PIEDA) scheme was used to estimate the binding energies of L-R complexes. We found that a strong salt bridge with D3.32 initiates the inhibition of the dopamine D4 receptor. This interaction also occurs in the binding of agonists, but the change in the receptor conformation to the active state starts with interaction with cysteine C3.36. Such a mechanism may arise in the case of agonists unable to form a hydrogen bond with the serine S5.46, considered, so far, to be crucial in the activation of GPCRs. The energy calculations using the FMO/PIEDA method indicate that antagonists show higher residue occupancy of the receptor binding site than agonists, suggesting they could form relatively more stable complexes. Additionally, antagonists were characterized by repulsive interactions with S5.46 distinguishing them from agonists.