Topological Analysis Of Electron Density Research Articles

DFT study on the Stereoselectivity of Asymmetric Synthesis of C, N‐Cyclic Azomethine Imines with Allyl Alkyl Ketones

AbstractBased on the density functional theory, the stereoselectivity of the asymmetric synthesis of tetrahydroisoquinolinopyrazole derivatives by the cycloaddition reaction of C, N‐cyclic azomethine imines with allyl alkyl ketones which was catalyzed using a chiral primary amine is studied theoretically. The results demonstrate that the four chiral transition states (TS‐1R2R, TS‐1R2S, TS‐1S2R and TS‐1S2S) are formed by the reaction of dienamine intermediate with C, N‐cyclic azomethine imine, and the reaction barrier of TS‐1R2S is in the lowest level (ΔG=6.98 kcal/mol). The consequence reveal that the 1R2S configuration product is formed by TS‐1R2S transition state. Non‐covalent interaction and electron density topology analysis show that the stereoselectivity of the chiral product is determined through van der Waals forces and hydrogen bond interaction of the transition state molecules.

Vibrational spectra, molecular structure, electronic, pharmaceutical and bonding nature of (4S)-4-(3,4-dihydroxyphenyl)-1,2,3,4-tetrahydroisoquinoline-7,8-diol - anti hypertension agent

Several factors, including environment, behaviours, and heredity, influence the development of hypertension. The title compound dopamine D1 receptor agonist named (4S)-4-(3,4-dihydroxyphenyl)-1,2,3,4-tetrahydroisoquinoline-7,8-diol (4S4D4T) is one of the most important neurotransmitters associated with numerous neural disorders. Using DFT and quantum chemical simulations, the vibrational, electrical, and structural possessions of the heading compound were predicted. To carry out the quantum computational investigations, a highly compatible method entitled B3LYP basis set was adopted. Vibrational Modes of functional groups with PED values were calculated using VEDA software to compute geometric dimensions and assign fundamental vibrations. Using gas and solvent phases, MEP differentiates between nucleophilic and electrophilic sites and creates distribution for the charge of the molecules. The observed wavelength with (TDSCF) UV–Vis spectra for the various solvents phases were compared. The NBO approach provides an understanding of the electron delocalization that results from hyperconjugation. FUKUI analysis is used to determine the area of site reaction. Electron density's topological analysis was carried out using the QTAIM theory. The ADME (Absorption, Distribution, Metabolism, Excretion) profiles are produced with the Swiss ADME online tool. In summary, this dissertation offers a thorough examination that evaluates the impact of particular pharmaceuticals on solvation and enzyme efficiency using a combination of spectral and quantitative computing methodologies. Therefore, plans for further research can profit immensely by the information gathered. The results of protein-ligand docking using the Auto Dock method with various proteins suggest that the molecule has pharmaceutical properties against receptors.

The cyanide, cyanate, thiocyanate ambident anions: Structure, topological analysis of electron density, and homolytic oxidative coupling regioselectivity

At the B3LYP/6-311++G(3df,3pd) level of theory, the spatial and electronic structure of the cyanide, cyanate and thiocyanate ambident anions has been studied. By means of the natural bond orbital (NBO) analysis and the R. F. W. Bader?s quantum theory ?Atoms in Molecules? (QTAIM), the electron density delocalization and topological properties in the above anions have been investigated. The distribution of electron density (NBO, QTAIM) in the XCN- (X = O, S) anions is reflected by the scheme [X-?C=?N]-. The relative contribution of the hypothetical structure X=C=N- to the resonance hybrid -X?C?N ?X=C=N- is higher in the case of X = O. The degree of the C?N or C=?N bond triple character and bond strength changes in the following series of anions: CN- > SCN- > OCN-. The occupancy of the lone electron pair (LP) orbital of the nitrogen atom in the above anions is close to 2, and the LP orbital is sp-hybridized. Condensed K. Fukui functions for the electrophilic attack have been evaluated. Local hardness of the donor reaction centres: N > C (CN-), O > N (OCN-), N > S (SCN-). The regioselectivity of the homolytic oxidative coupling reactions of CN-, OCN-, SCN- has been substantiated.

Structure, stability and reactivity of inverse sandwich complexes M‐Be3‐M and M‐Zn3‐M (M = Li, Na, K, Cu, Ag, Au)

AbstractQuantum chemical calculations have b‐een carried out on the inverse sandwich type complexes formed between coinage and alkali metals with Be3 and Zn3 rings. Calculations reveal that the complexes are stable toward dissociation. Their Lewis acidic character has been evaluated using fluoride ion affinity (FIA) calculation, which reveals their strong acidic character. Topological analysis of electron density has also been performed to investigate the nature of the bond between the metal and the fluoride ion. Calculations reveal non covalent nature in case of alkali series and covalent nature in case of coinage metal series.

B-carboranyl methyl thioether ligands in coordination with the W(CO)5 fragment

Complexation of B-closo- and nido-carboranyl methyl thioethers with the pentacarbonyltungsten fragment was studied. An unusual instability of the nido-derivative is detected and rationalized by means of the quantum chemical calculations followed by the topological analysis of electron density and the Interacting Quantum Atoms analysis. The structure of {(CO)5W[9-MeS-1,2-C2B10H11-κ1-S(1)]} was determined by single crystal X-ray diffraction.

Halogen Bond-Involving Self-Assembly of Iodonium Carboxylates: Adding a Dimension to Supramolecular Architecture.

We designed 0D, 1D, and 2D supramolecular assemblies made of diaryliodonium salts (functioning as double σ-hole donors) and carboxylates (as σ-hole acceptors). The association was based on two charge-supported halogen bonds (XB), which occurred between IIII sites of the iodonium cations and the carboxylate anions. The sequential introduction of the carboxylic groups in the aryl ring of the benzoic acid added a dimension to the 0D supramolecular organization of the benzoate, which furnished 1D-chained and 2D-layered structures when terephthalate and trimesate anions, correspondingly, were applied as XB acceptors. The structure-directing XB were studied using DFT calculations under periodic boundary conditions and were followed by the one-electron-potential analysis and the Bader atoms-in-molecules topological analysis of electron density. These theoretical methods confirmed the existence of the XB and verified the philicities of the interaction partners in the designed solid-state structures.

Organometallic Allene [(μ-C)(Fe(CO)4 )2 ]: Bridging Carbon Showing Transformation from Classical Electron-Sharing Bonding to Double σ-Donor and Double π-Acceptor Ligation.

Allenes (R2 C=C=CR2 ) have been traditionally perceived to feature localized orthogonal π-bonds between the carbon centres. We have carried out quantum-mechanical studies of the organometallic allenes envisioned by the isolobal replacement of the terminal CH2 groups by the d8 Fe(CO)4 fragment. Our studies have identified two organometallic allenes viz. D2d symmetric [(μ-C)(Fe(CO)4 )2 ] (2) and D3 symmetric [(μ-C)(Fe(CO)4 )2 ] (3) with trigonal bipyramidal coordination at the Fe atoms. Compound 2 features the bridging carbon atom in an equatorial position with respect to the ligands on the TM centre, while 3 features the central carbon atom in an axial position. The bis-pseudoallylic anionic delocalisation proposed in the C2-C1-C3 spine of organic allene is retained in the organometallic allene 2, and is transformed to a typical three-centre bis-allylic anionic delocalisation in the organometallic allene 3. The topological analysis of electron density also indicates a bis-allylic anionic type delocalisation in the organometallic allenes. The quantitative bonding analysis using the EDA-NOCV method suggests a transition from classical electron-sharing bonding between the central carbon atom and the terminal groups in 1 to donor-acceptor bonding in 3. Meanwhile, both electron-sharing and donor-acceptor bonding models are found to be probable heuristic bonding representations in the organometallic allene 2.

New Complexes of Antimony(III) with Tridentate O,E,O-Ligands (E = O, S, Se, Te, NH, NMe) Derived from N-Methyldiethanolamine.

We synthesized a series of new antimony(III) compounds by reaction of Sb(OEt)3 with organic ligands of the type E(CH2-CH2-OH)2, with E = NH, NMe, O, S, Se, and Te. The synthesized compounds have the general composition [E(CH2-CH2-O)2]Sb(OEt). For comparison, the compound (O-CH2-CH2-S)Sb(OEt) was prepared. All compounds are characterized using NMR, IR, and Raman spectroscopy. The molecular structures of the products reveal the formation of chelate complexes, wherein the ligand molecules coordinate as tridentate O,E,O-ligands to the antimony atom. Dimer formation in the solid state allows the antimony atoms to reach pentacoordination. Quantum chemical calculations including topological analysis of electron density reveal that there are polar shared bonds between antimony and the oxygen atoms bound to antimony. The interactions between the donor atom E and the Sb atom and the interactions in the dimers can be characterized as Van der Waals interactions. The reactivity of [MeN(CH2-CH2-O)2]Sb(OEt) was investigated as an example. For this purpose, the compound reacted with a range of organic compounds such as carboxylic acids and carboxylic anhydrides and small molecules like CO2 and NH3. This study establishes a new and easy accessible class of antimony(III) compounds, provides new insights into the chemistry of antimony compounds and opens up new opportunities for further research in this field.

Comparison of experimental and theoretical spectral groups, electronic properties, topological, and molecular docking investigations of 1-N-Cbz-piperidine-4-carboxylic acid- Potential Cancer drug

In this present work, the theoretical and experimental spectroscopic (FT-IR, FT-Raman) investigations were performed for 1-N-Cbz-piperidine-4-carboxylic acid (1NCPA). The theoretical approaches were computed using Density Functional Theory (DFT)/ B3LYP/6–311++G(d,p) as a basis set. Using the aforementioned basis set, the optimized molecular geometrical parameters and computed wavenumbers were determined. The theoretical (TD-SCF) UV–Vis's spectra for the solvent phases and recorded wavelength were compared to one another. Frontier molecular orbitals (energy parameters), hole-electron distribution for the excited states, and ESP analyses were reported. The QTAIM theory was used to accomplish the topological analysis of electron density. Further, ELF, LOL, and RDG analyses were reported. The title compound (as a ligand) and ALK inhibitors (as protein) with their bonding interactions were studied using molecular docking analysis. It was compared with the standard drug and the least binding energy was calculated.

Structural and theoretical study of π-stacking interactions in new complexes based on CuCl2 and 3-sulfonamide-substituted imidazo[2,1-b]thiazoles.

At present, sulfonamides and their metal complexes have received a new impetus for development. Of particular interest is the study of molecular and crystal structures, which takes into account weak non-valent interactions. Despite the low energy of such interactions, in many cases, they act collectively, and the sum of their actions can play a significant role. As a result, the spectrum of medical and biological activity of new metal complexes is expanded. In this regard, the synthesis and study of the molecular and crystal structure of sulfonamides and their metal complexes is of undoubted relevance. In this work, we studied non-valent intra- and intermolecular interactions in ligands of sulfonamide-substituted imidazo[2,1-b]thiazoles and their previously unknown complexes with CuCl2. The performed analysis of the data obtained by X-ray diffraction analysis made it possible to establish the intramolecular π-stacking interaction in imidazothiazole ligands, which is retained in their complexes with CuCl2. Within the framework of QTAIM topological analysis of electron density and DORI analysis, stereoelectronic and topological structures were studied. In the complexes, tetral, chalcogen, and pnycogen new interligand non-valent interactions were established. The energies of all established types of non-valent interactions have been calculated, and their comparative evaluation has been made. X-ray data of new arylsulfonylamino-substituted derivatives of imidazo[2,1-b]thiazoles and their metal complexes with CuCl2 have been studied. To determine the theoretical prerequisites for the occurrence of π-stacking in the molecules under study, the QTAIM method was used in the framework of the DFT/B3LYP/6-311 + G(d) calculation using the GAUSSIAN 09 program. In addition, the DORI electron density region overlap indicator and the Multiwfn program were used to analyze non-valent interactions.

On the Nature of the Partial Covalent Bond between Noble Gas Elements and Noble Metal Atoms

This article provides a discussion on the nature of bonding between noble gases (Ng) and noble metals (M) from a quantum chemical perspective by investigating compounds such as NgMY (Y=CN, O, NO3, SO4, CO3), [NgM-(bipy)]+, NgMCCH, and MCCNgH complexes, where M=Cu, Ag, Au and Ng=Kr-Rn, with some complexes containing the lighter noble gas atoms as well. Despite having very low chemical reactivity, noble gases have been observed to form weak bonds with noble metals such as copper, gold, and silver. In this study, we explore the factors that contribute to this unusual bonding behavior, including the electronic structure of the atoms involved and the geometric configuration of the concerned fragments. We also investigate the metastable nature of the resulting complexes by studying the energetics of their possible dissociation and internal isomerization channels. The noble gas-binding ability of the bare metal cyanides are higher than most of their bromide counterparts, with CuCN and AgCN showing higher affinity than their chloride analogues as well. In contrast, the oxides seem to have lower binding power than their corresponding halides. In the oxide and the bipyridyl complexes, the Ng-binding ability follows the order Au > Cu > Ag. The dissociation energies calculated, considering the zero-point energy correction for possible dissociation channels, increase as we move down the noble gas group. The bond between the noble gases and the noble metals in the complexes are found to have comparable weightage of orbital and electrostatic interactions, suggestive of a partial covalent nature. The same is validated from the topological analysis of electron density.

Charge-Shifted Weak Noncovalent Interactions in the Atmospherically Important OCS Microhydrates.

Stratospheric aerosol, mainly comprising microhydrated carbonyl sulfide (OCS), is among the primary drivers of climate change. In this study, we investigate the effect of microhydration on the structure, energetics, and vibrational properties of the neutral OCS molecule using ab initio calculation, molecular electrostatic potential (MESP), topological analyses of electron density, and natural bond orbital (NBO) analyses. The complexation energy increases with the cluster size, and the first solvation shell of OCS consists of four water molecules that interact with the OCS moiety preferentially through SOCS···OW, OOCS···OW, and COCS···OW type of weak noncovalent interaction instead of the typical OOCS···H-OW and SOCS···H-OW H-bonds. These noncovalent interactions originate due to the electron shift from the water oxygen lone pair to the antibonding orbital of C═S [BD*(C═S)], sometimes via BD*(C═O), which substantially perturbs the bending mode of surrounding water molecules. The present study thus unravels the underlying relationship between the OCS atmospheric hydrolysis and the charge-shifted noncovalent interactions.

Mechanism study on H2S capture of ionic liquids based on triethylenetetramine blended with ethylene glycol

Amino-functionalized ILs are promising absorbents for H2S. In this work, three triethylenetetramine functionalized ionic liquids (TETAH-ILs) were synthesized and applied to construct mixture solutions with ethylene glycol (EG). Among [TETAH][HCOO]-EG, [TETAH][BF4]-EG and [TETAH]Br-EG absorbents, [TETAH][BF4]-EG showed the greatest H2S absorption capacity. In addition, a series of factors, such as IL molar fraction, absorption temperature and H2S flow rate, were also investigated to evaluate the effects on absorption performance of [TETAH][BF4]-EG absorbent. The results showed that the 10 % [TETAH][BF4]-EG mixed solution has excellent absorption capacity (1.128 mol H2S/mol IL) at 303.15 K and 100 mL/min. In addition, the absorbent could remain 75.12 % absorption capacity after four regenerations, which displayed potential for reversibility. Furthermore, the mechanism of H2S absorption by TETAH-ILs was proposed by combining FT-IR and 1H NMR characterization and electron density topology analysis. Furthermore, the mechanism of H2S absorption by TETAH-ILs was proposed by combining FT-IR and 1H NMR characterization and theoretical calculation. The results revealed that the mechanism of H2S absorption by TETAH-ILs was the formation of IL-H2S complexes through a series of hydrogen bonds.

Anti-Symmetric Electromagnetic Interactions' Response in Electron Circular Dichroism and Chiral Origin of Periodic, Complementary Twisted Angle in Twisted Bilayer Graphene.

Many novel physical properties of twisted bilayer graphene have been discovered and studied successively, but the physical mechanism of the chiral modulation of BLG by a twisted angle lacks theoretical research. In this work, the density functional theory, the wavefunction analysis of the excited state, and the quantum theory of atoms in molecules are used to calculate and analyze the anti-symmetric chiral characteristics of zigzag-edge twisted bilayer graphene quantum dots based on periodic complementary twisted angles. The analysis of the partial density of states shows that Moiré superlattices can effectively adjust the contribution of the atomic basis function of the fragment to the transition dipole moment. The topological analysis of electron density indicates that the Moiré superlattices structure can enhance the localization of the system, increasing the electron density of the Moiré central ring, reducing the electron surge capacity in general and inducing the reversed helical properties of the top and underlying graphene, which can be used as the origin of the chiral discrimination; it also reveals the mole in the superlattice chiral physical mechanism. On this basis, we will also study the nonlinear optical properties of twisted bilayer graphene based on a twisted angle.

On the influence of pnictogen bonding on acidity

The pnictogen-bonded systems with general formula – HA/PnX3 (where HA = HBr, HCl, H2O, NH3, CH3NH2, (CH3)2NH, Pn = P, As, Sb, Bi, X = H, F) were investigated with the aim of assessing the influence of the electron density flow upon the pnictogen bond formation on the acidity of resulting system. The results of calculations indicate that said influence is significant in most cases. The formation of HA/PnX3 pnictogen bonded acid may be assisted by creation of hydrogen bonds leading to a further increase in acidity. As measured by the bond degree parameter, pnictogen bonds formed by the studied systems were found to exhibit a covalence degree higher than that of hydrogen bonds. The relationship between the structure and acidity was elucidated with the use of the electron density topology analysis.

Enhancing first-principles simulations of complex solid-state ion conductors using topological analysis of procrystal electron density

Atomistic-level understanding of ion migration mechanisms holds the key to design high-performance solid-state ion conductors for a breadth of electrochemical devices. First-principles simulations play an important role in this quest. Yet, these methods are generally computationally-intensive, with limited access to complex, low-symmetry structures, such as interfaces. Here we show how topological analysis of the procrystal electron density can be applied to efficiently mitigate this issue. We discuss how this methodology goes beyond current state of the art capabilities and demonstrate this with two examples. In the first, we examine Li-ion transport across grain boundaries in Li3ClO electrolyte. Then, we compute diffusion coefficients as a function of charge carrier concentration in spinel LiTiS2 electrode material. These two case studies do not exhaust the opportunities and might constitute motivations for still more complex applied materials.

The Distance between Minima of Electron Density and Electrostatic Potential as a Measure of Halogen Bond Strength.

In this study, we present results of a detailed topological analysis of electron density (ED) of 145 halogen-bonded complexes formed by various fluorine-, chlorine-, bromine-, and iodine-containing compounds with trimethylphosphine oxide, Me3PO. To characterize the halogen bond (XB) strength, we used the complexation enthalpy, the interatomic distance between oxygen and halogen, as well as the typical set of electron density properties at the bond critical points calculated at B3LYP/jorge-ATZP level of theory. We show for the first time that it is possible to predict the XB strength based on the distance between the minima of ED and molecular electrostatic potential (ESP) along the XB path. The gap between ED and ESP minima exponentially depends on local electronic kinetic energy density at the bond critical point and tends to be a common limiting value for the strongest halogen bond.

The Complexation between Siloxane Species and Methylsiloxane: Electronic Structure, Thermodynamic, and Interaction Characteristics

AbstractThe interaction between organosiloxane materials and siloxane species has attracted extensive attention in the protection of cultural relics due to their bonding characteristics. In this context, detailed studies of the complexation between siloxane species and methylsiloxane were explored using various computational methods. The complex molecular structures and their electronic excitation characteristics were predicted. The strong covalent interactions of Si−O bond between siloxane and methylsiloxane are checked by topological analysis of electron density and obvious charge transfer. Thermodynamic results show that these types of complexes are considerable stability. The energy barrier of oxygen molecules to pass through the pores between methylsiloxane and silica close to 19 eV, indicating that this type of coating does not peel off easily. Moreover, IR and UV‐vis spectrum were predicted. The microscopic mechanism will give theoretical direction for theoretical guidance for practical applications of the coating in the protection of stone artifacts.

Missing Recipe in the Na‐B Bond in NaBH3–Cluster

AbstractThe multifaceted little Na−B bond in NaBH3‐cluster has been the subject of many recent studies. Many proposals have been put forward for the complete understanding of the chemical bonding in NaBH3‐cluster. However, none of the studies provided a complete picture. Herein, the missing recipe of the chemical bonding in NaBH3‐cluster has been identified which completes the description. Our calculations reveal that the chemical bonding in NaBH3‐cluster is more multifaceted than ever thought. Our finding suggests that the NaBH3‐cluster features a Na−B one electron bond which is assisted by three 3‐centre‐2‐electron Na‐B−H bond. Detailed topological analyses of electron density and electron localization function at the correlated level reveal such a bonding situation. This missing 3‐centre‐2‐electron Na‐B−H bond completes the description of chemical bonding in NaBH3‐cluster which is at‐per with the well established bonding scenario for electron deficient compounds. Similar bonding scenario is observed in KBH3−, CuBH3‐and AuBH3−clusters, further lending support to the complete picture of bonding.

Origin of the low formation energy of oxygen vacancies in CeO2

Oxygen vacancies play a crucial role in determining the catalytic properties of Ce-based catalysts, especially in oxidation reactions. The design of catalytic activity requires keen insight into oxygen vacancy formation mechanisms. In this work, we investigate the origin of oxygen vacancies in CeO2 from the perspective of electron density via high-energy synchrotron powder x-ray diffraction. Multipole refinement results indicate that there is no obvious hybridization between bonded Ce and O atoms in CeO2. Subsequent quantitative topological analysis of the experimental total electron density reveals the closed-shell interaction behavior of the Ce–O bond. The results of first-principles calculation indicate that the oxygen vacancy formation energy of CeO2 is the lowest among three commonly used redox catalysts. These findings indicate the relatively weak bond strength of the Ce–O bond, which induces a low oxygen vacancy formation energy for CeO2 and thus promotes CeO2 as a superior catalyst for oxidation reactions. This work provides a new direction for design of functional metal oxides with high oxygen vacancy concentrations.