Atoms In Molecules Analysis Research Articles

Fused 1,2-Diboraoxazoles Based on closo-Decaborate Anion-Novel Members of Diboroheterocycle Class.

The novel members of the 1,2-diboraoxazoles family have been obtained. In the present work, we have carried out the intramolecular ring-closure reaction of borylated iminols of general type [B10H9N=C(OH)R]− (R = Me, Et, nPr, iPr, tBu, Ph, 4-Cl-Ph). This process is conducted in mild conditions with 83–87% yields. The solid-state structures of two salts of 1,2-diboraoxazoles were additionally investigated by X-ray crystallography. In addition, the phenomena of bonding interactions in the 1,2-diboraoxazole cycles have been theoretically studied by the Quantum Theory of Atoms in Molecules analysis. Several local and integral topological properties of the electron density involved in these interactions have been computed.

Theoretical studies on the electronic and optoelectronic properties of DNA/RNA hybrid-metal complexes

The electronic and optoelectronic properties of DNA/RNA functionalized conductive metal adatoms were studied using DFT and TDDFT methods. Four hybrid structures were selected from the experimental work on RNA microchips. The occupied number of states by the system at each energy level were studied by Density of States (DOS). Atom-in Molecules (AIM) analysis and Noncovalent Interaction (NCI) PLOT were used to study the interaction in these complexes. Results indicated that HOMO-LUMO (HL) Gap is larger for C1–C4 complexes as compared to the HL gap for DNA/RNA hybrid-metal interacted complexes. This clearly indicates strong DNA/RNA-metal interaction, which is also observed in NCIPLOT analysis. Al and Au are chemically bonded to DNA/RNA hybrids, while the adsorption of Cu is between weak chemisorption and strong physisorption. The interacted bond distance of DNA/RNA-(Al, Cu) complexes are smaller than the bond distance of DNA/RNA-Au complexes. AIM analysis predicts noncovalent interaction for the studied complexes. TDDFT results indicate that few complexes can be used as fluorescent biomarkers as the absorption and emission wavelength lies in the visible region.

Non-covalent Interactions Directed Rearrangement of Lactones to Pyrones: A Computational Study on the Mechanistic Insights of Solvent Assisted Gold(I) Catalyzed Reactions

The mechanism of gold(I) catalyzed cycloisomerization of lactones to pyrones was analyzed by performing DFT study using B3LYP method with LanL2DZ basis set for Au and 6-31g(d) basis set for all other atoms. The potential energy surface of the reaction was scanned to know the preferred path for the formation of products under gas phase. The effects of solvent using acetonitrile, dichloromethane and toluene are explored as these solvents are reported to play a crucial role in the final product formation. The crossover between the oxophilic and alkynophilic reaction complexes, R-O and R-C, is found to be the major driving force which directs the product formation. While the larger energy gap between R-O and R-C leads to pyrone formation, the smaller difference and in turn the rapid crossover between R-O and R-C leads to the formation of decarboxylation adduct. Counterion plays a major role throughout the reaction. The atoms in molecules analysis on R-C using implicit as well as explicit solvent gave reason for the observed experimental trends and suggest that the prevailed non-covalent interactions play a substantial role in the product formation.

Sensing of toxic Lewisite (L1, L2, and L3) molecules by graphdiyne nanoflake using density functional theory calculations and quantum theory of atoms in molecule analysis

AbstractPromising sensor applications of graphdiyne for various gases and toxic molecules have extensively been studied; however, similar studies for the detection of chemical warfare agents (CWA) are not reported. Here, we report the adsorption of Lewisites (L1, L2, and L3), on graphdiyne nanoflake (GDY) using density functional theory (DFT) ωB97XD/6‐31+G (d,p) method. Our results show that Lewisite molecules are preferably physiosorbed at the triangular portion of GDY nanoflake. In particular, the binding of L3(3‐chlorovinyl arsine) on GDY nanoflake is thermodynamically favorable than L1(1‐chlorovinylarsonous dichloride) and L2(2‐chlorovinylarsonous chloride). Symmetry adopted perturbation theory (SAPT0) analysis reveals that the least contribution of repulsive exchange component is present in case of L2@GDY complex. Further, the smallest HOMO‐LUMO energy gap, appreciable charge transfer (NBO), and largest red shift in ultraviolet‐visible (UV‐Vis) spectrum are also in accord with the higher %sensitivity of graphdiyne toward L2. Quantum theory of atom in molecule (QTAIM) analysis is performed to get insight into the noncovalent interactions. Therefore, it is predicted that the sensitivity of GDY nanoflake is potentially high for Lewisite especially for L2.

Computational study of phosphate adsorption on Mg/Ca modified biochar structure in aqueous solution

Phosphate removal in water using biochar is widely investigated. Density functional theory was used to study the adsorption of phosphate (H2PO4−) on biochar in water after metal modification. Two types of metals, Mg and Ca, were used to modify the biochar structure, and the edge and metal adsorptions of H2PO4− were investigated on the modified biochar structure. Results were analyzed from the aspects of structural stability, adsorption energy, change in dipole moment, density of electronic states, and atoms in molecules analysis. The overall effect of metal-modified biochar materials on phosphate adsorption was stronger than that of unmodified biochar materials in terms of molecular level. The stability of the metal-modified structure by adding metal was low, and adsorption was prone to occur in this situation. The Ca-modified biochar showed better phosphate adsorption than the Mg-modified structure. Metal adsorption performed better than edge adsorption, proving that the modified metal in the biochar structure played a leading role in H2PO4− adsorption. Metal adsorption was mainly caused by electrostatic attraction, and edge adsorption was mainly caused by covalent bonding.

Main-Group Metals Stabilized Polypyrrolic Uranyl(V) Complexes via Cation-Cation Interaction with the Uranyl exo-Oxo Atom: A Relativistic Density Functional Theory Study.

To explore the innovative uranyl(V) complexes by deeply understanding their coordination stability, relativistic density functional theory calculations have been performed to investigate the experimentally reported [(py)(R2AlOUVO)(py)(H2L)] [R = Me (1), iBu (2)] and [{(py)3MOUVO}(py)(H2L)] [M = Li (3), Na (4), K (5)] and their uranyl(VI) counterparts. Structural and topological analyses along with transformation-reaction energies and redox potentials were systematically studied. Geometrical and quantum theory of atoms in molecules analyses implied a linear U-Oexo-M feature in 1-3 and a bent one in 4 and 5. The calculated free energies (ΔrG) of reactions transforming 1/2 into 3/4/5 confirmed a higher stability of the latter ones, which were further corroborated by their reduction potentials (E0). The E0 value of 5 versus uranyl(VI) is close to its experimental value, particularly in solvation with spin-orbit coupling. The highest occupied and lowest unoccupied molecular orbitals of uranyl(V) and uranyl(VI) have predominant U(5fδ) character. Compared to mononuclear uranyl(VI), the coordination of aluminum and alkali metals to uranyl exo-oxo significantly contributes to the stabilization of uranyl(V) by altering the E0 value from -1.59 to -0.85, -0.91, -1.33, -1.50, and -1.46 V, respectively. The calculation results show a more positive E0 than that of the precursor 6VI/6 without exo-oxo coordination. The calculated E0 values of 3-5 are certainly more negative than those of 1 and 2. The alkali metals were found to activate U═O bonds more easily/readily than aluminum by coordination to the exo-oxo atom. In brief, the uranyl exo-oxo cation-cation-interaction enhanced the reduction ability from its uranyl(VI) analogue and raised the stability of the UV center.

Acidity enhancement of α‐carbon of beta diketones via hydroxyl substituents: A density functional theory study

AbstractDensity functional theory method and B3LYP/6‐311++G(d,p) level of theory were used to determine the acidity of α‐carbon in the hydroxyl derivatives of beta diketones in the gas phase. An investigation of acidity strength in the gas phase indicates that α‐carbon of hydroxyl derivatives of beta diketones become stronger acids than the α‐carbon of beta diketone itself as their conjugate bases gain more stability via both enolate and hydrogen bond formation. Natural bond orbital and quantum theory of atoms in molecules analyses also confirm the role of hydrogen bond interactions on increasing the acidity of α‐carbon of hydroxyl derivatives of beta diketones.

Analysis of Bonding Properties of Osmabenzyne in the Ground State (S0) and Excited Singlet (S1) State: A Quantum-Chemical Calculation

The hybrid density functional MPW1PW91 theory was applied in the ground state (S0) and first excited singlet (S1) state to highlight the structure, electronic properties, and aromaticity of an osmabenzyne complex. The first singlet excited state was determined by time-dependent DFT (TD-DFT) method. It was tried to explore the geometry, frontier orbital energies, reactivity indices, and aromaticity in the first singlet excited state of osmabenzyne complex and compare to ground state. Moreover, this study determined the involvement of the fragments of the studied complexes in the frontier orbitals regarding the ground state and first singlet excited state. Energy decomposition analysis (EDA) for S0 and S1 states was applied to study the nature of the chemical bond between the [Os (PH3)2Cl2]2+ and [C5H4]2– fragment. ‎In addition, the Os–C, Os–Cl, and Os–P bonds in the studied osmabenzyne were clarified using quantum theory of atoms in molecules analysis (QTAIM) calculations.

Experimental and Computational Investigations of Carboplatin Supramolecular Complexes.

Supramolecular systems (macromolecules), such as calix[n]arenes (SCn), cyclodextrins (CDs), and cucurbiturils (CBs), are promising vehicles for anticancer drugs. In this work, guest–host complexes of carboplatin, a second-generation platinum-based anticancer drug, and p-4-sulfocalix[n]arenes (n = 4 and 6; PS4 and PS6, respectively) were prepared and studied using 1H NMR, UV, Job’s plot analysis, HPLC, and density-functional theory calculations. The experimental and the computational studies suggest the formation of 1:1 complexes between carboplatin and each of PS4 and PS6. The stability constants of the formed complexes were estimated to be 5.3 × 104 M–1 and 9.8 × 104 M–1, which correspond to free energy of complexation of −6.40 and −6.81 kcal mol–1, in the case of PS4 and PS6, respectively. The interaction free energy depends on the different inclusion modes of carboplatin in the host cavities. UV–vis findings and atoms in molecules analysis showed that hydrogen bond interactions stabilize the host–guest complexes without the full inclusion in the host cavity. The in vitro anticancer study revealed that both complexes exhibited stronger anticancer activities against breast adenocarcinoma cells (MCF-7) and lung cancer cells (A-549) compared to free carboplatin, preluding to their potential use in cancer therapy.

La(III), Ce(III), Gd(III), and Eu(III) Complexation with Tris(hydroxymethyl)aminomethane in Aqueous Solution.

Lanthanides such as cerium(III), europium(III), and gadolinium(III) are widely used for designing fluorescent probes or magnetic resonance imaging contrasting agents for biological systems. The synthesis and study of lanthanide complexes in buffer solutions imitating biological fluids are often complicated because of a lack of data on the lanthanide interactions with buffer solution components. Therefore, Ln(III) [where Ln(III) = La(III), Ce(III), Gd(III), Eu(III)] complexation with a widely used buffer agent, tris(hydroxymethyl)aminomethane (Tris), in aqueous solution is studied using potentiometry, spectrofluorimetry, and 139La NMR spectroscopy. The stoichiometric composition of complexes is determined using mass spectrometry. The thermodynamic stability constants of Ln(III)-Tris complexes are calculated from potentiometric and spectral data; the difficulties in the study of these systems, reliability, and accuracy of the obtained constants are discussed. The possible structures of free Tris and its complexes with lanthanides(III) are optimized on the density functional theory/PBE0 level; the peculiarities of metal-ligand bonds were studied by Quantum Theory Atoms in Molecules analysis.

QUANTUM-CHEMICAL INVESTIGATION OF THE COMPLEXATION OF TITANOCENE DICHLORIDE WITH C20 AND M+@C20 (M+ = Li, Na, K) CAGES

In this study, the interaction of titanocene dichloride with C20 and M+@C20 (M+ = Li+, Na+, K+) cages is investigated using quantum mechanical methods. The M06-2X functional and the 6-311G(d,p) basis set are applied in these calculations. The bonding interactions between the C20 and M+@C20 clusters with the titanocene dichloride complex are examined through the energy decomposition analysis. The charge transfer between fragments is illustrated by the electrophilicity-based charge transfer (ECT). Also, the thermodynamic parameters of these interactions are calculated. Finally, the quantum theory of atoms in molecules analysis is used to assess BCP(C–Cl) within the C20 and M+@C20… titanocene dichloride complexes.

Synthesis, Crystal Structure, and Computational Methods of Vanadium and Copper Compounds as Potential Drugs for Cancer Treatment.

Transition metal-based compounds have shown promising uses as therapeutic agents. Among their unique characteristics, these compounds are suitable for interaction with specific biological targets, making them important potential drugs to treat various diseases. Copper compounds, of which Casiopeinas® are an excellent example, have shown promising results as alternatives to current cancer therapies, in part because of their intercalative properties with DNA. Vanadium compounds have been extensively studied for their pharmacological properties and application, mostly in diabetes, although recently, there is a growing interest in testing their activity as anti-cancer agents. In the present work, two compounds, [Cu(Metf)(bipy)Cl]Cl·2H2O and [Cu(Impy)(Gly)(H2O)]VO3, were obtained and characterized by visible and FTIR spectroscopies, single-crystal X-ray diffraction, and theoretical methods. The structural and electronic properties of the compounds were calculated through the density functional theory (DFT) using the Austin–Frisch–Petersson functional with dispersion APFD, and the 6-311 + G(2d,p) basis set. Non-covalent interactions were analyzed using Hirshfeld surface analysis (HSA) and atom in molecules analysis (AIM). Additionally, docking analysis to test DNA/RNA interactions with the Casiopeina-like complexes were carried out. The compounds provide metals that can interact with critical biological targets. In addition, they show interesting non-covalent interactions that are responsible for their supramolecular arrangements.

Energetically significant nitrile⋯nitrile and unconventional C–H⋯π(nitrile) interactions in pyridine based Ni(II) and Zn(II) coordination compounds: Antiproliferative evaluation and theoretical studies

Two new coordination compounds viz. [Ni(2,6-PDC)(Hdmpz)(H2O)2]∙H2O (1) and [Zn(3-CNpy)2Cl2] (2) (2,6-PDC = 2,6-pyridinedicarboxylate, Hdmpz = 3,5-dimethylpyrazole, 3-CNpy = 3-cyanopyridine) have been synthesized and characterized using elemental analysis, thermogravimetric analysis, electronic, infrared spectroscopy and single crystal X-ray diffraction techniques. Crystal structure analyses reveal the presence of supramolecular assemblies involving interesting dimers with unconventional contacts in the compounds. DFT (Density Functional Theory) calculations on the supramolecular dimers in the crystal structure of 1 reveal that the sum of contributions of anion–π, π–π and other long range interactions due to the approximation of the bulk monomers is energetically significant. Molecular Electrostatic Potential (MEP) surface and Quantum Theory of Atoms in Molecules (QTAIM) analyses on the interesting supramolecular dimers of the crystal structures of 2 reveal the presence of unconventional anion⋯π contacts involving coordinated chlorido ligands and C–H⋯π(nitrile) interactions involving the π-system of the nitrile moiety of 3-cyanopyridine. Remarkably, Atoms in Molecules analysis also confirms the existence of energetically significant unconventional anti-parallel nitrile⋯nitrile interaction in the crystal structure of 2. Cell cytotoxicity of the compounds performed in Dalton's lymphoma (DL) malignant cancer cell line showed effective potency with negligible cytotoxicity in normal cells (~12%). It is interesting that compound 1has excellent cytotoxic potency with IC50 closer to cisplatin and can bind different biological targets with similar signalling pathways. Structure activity relationship (SAR) analyses of 1 and 2 based on pharmacophore modelling reveal that the molecular features associated with the structures of the compounds play important role in the biological activities.

A theoretical insight into the reducing properties of bicyclic dithia hydrocarbons and hetero-bicyclic dithiolopyrrolone compounds with rotation-restricted planar disulfide linkage

The current study primarily involves the investigation of reducing properties of dithia-substituted bicyclic hydrocarbons. Adiabatic electron affinities (AEA) of the selected dithiabicyclic systems were investigated under gas and aqueous phase conditions. Calculated AEA values suggest the neutral-anion radical of the systems to be a perfect redox couple similar to cystines. Higher affinity to capture an electron is obtained in the aqueous environment. Natural bond orbital and atoms in molecule analyses were performed to obtain insight into the S–S bonding properties. One electron added radicals with elongated disulfide linkage indicates the viability of the systems towards rupturing upon reduction making it more suitable in drug carrier designing. The current investigation is also extended to biologically important dithiolopyrrolone (DTP) class of compounds and compared with dithiabicyclic hydrocarbons. The AEA range for neutral DTPs is found to be higher indicating more tendency of these systems to get reduced.

Density functional theoretical tailoring of electronic effect through various substituents on calix[4]arene‐crown‐6 for efficient Cs+ ion encapsulation and extraction

AbstractThe structure, energetic, and quantum chemical descriptors of Cs+ complexes of calix[4]arene‐crown‐6 (C4C6) and substituted C4C6, that is, 1,3 alternate‐diethoxy C4C6, are reported here based on the analysis of results obtained using density functional theory (DFT). Substitution of benzo group in both C4C6 and 1,3 alternate‐diethoxy C4C6 resulted in a reduction of binding energy (BE). Further substitution of the benzo group with methyl, methoxy, and amino groups leads to an increase in BE, and nitro substitution leads to decrease in BE for C4C6, whereas in the case of 1,3 alternate‐diethoxy calix[4]arenebenzocrown‐6, methoxy substitution leads to the highest BE compared to other complexes. The calculated Gibbs free energy, ΔGgas also followed the same order as BE in the case of 1,3 alternate‐diethoxy C4C6 and their substituted ligands. Furthermore, the ΔG of complexation was computed using a thermodynamic cycle with conductor‐like screening model in different solvents: toluene, chloroform, octanol, and nitrobenzene. The values of ΔGext are found to be increased with an increase in the dielectric constant of the solvent and were found to be highest in the nitrobenzene. The atoms in molecule analysis reveals partial ionic character in the CsO bond. Among all the studied complexes, 1,3 alternate‐diethoxy calix[4]arene 3′‐methoxy benzo crown‐6 displays highest ΔGext in nitrobenzene. The calculated value of ∆∆Gext (∆∆G = ∆GCs+ − ∆GNa+) is found to be −41.82 kcal/mol with 1,3 alternate‐diethoxy calix[4]arene 3′‐methoxy benzocrown‐6, which is higher than that obtained with calix [4] bis‐crown‐6 (−5.24 kcal/mol). The newly designed ligand might be suitable for the selective extraction of Cs+ over Na+ in the reprocessing of nuclear waste and thus invites experimentalists to test this DFT finding in the laboratory.

Interaction of modified nucleic bases with graphene and doped graphenes: a DFT study

In order to design biosensors, it is quite necessary to have an insight upon the nature of interaction between the modified nucleic bases (MNBs) and carbonaceous materials. This study is focussed upon the interaction of the various doped graphene models like graphene (GR), aluminium doped graphene (AlG), sulphur doped graphene (SG), nickel doped graphene (NiG), chromium doped graphene (CrG) and germanium doped graphene (GeG) with MNBs (caffeine, hypoxanthine, uric acid and xanthine) by employing the electronic structure calculations and the associated methodology. All the geometries considered in this study (MNBs and graphene models) were initially optimized at M06-2X/6-31+G** basis set without any constraints followed by the single point energy calculation at three different and well established methods using the Gaussian 09 software package. A detailed comparison of the interaction energy is accomplished in this study. The interaction energy values were further corrected for the basis set superposition error. The theory of atoms in molecules analysis is also performed in detail, which showcases the bond critical points, Laplacian and various other parameters of interest. The variation of frontier molecular orbitals, i.e., highest occupied molecular orbital–lowest unoccupied molecular orbital gap for different models of graphene have been discussed in detail upon the adsorption of MNBs. Among the doped graphene models, the graphene model doped with Cr seems to be more suitable for the application of sensors, also it is found that the MNBs interact primarily via $$\pi $$ – $$\pi $$ interaction. The results highlight that the CrG can act as a sensor for the detection of MNBs.

A combined molecular dynamics and quantum mechanics study on the interaction of Fe3+ and human serum albumin relevant to iron overload disease

The interaction of Fe3+ with blood proteins is very important because it leads to understanding the detrimental effect in biological processes. Molecular dynamic (MD) simulations and quantum chemistry calculations were performed to investigate the complex formation between the human serum albumin (HSA) and Fe3+. MD simulation results predict two binding sites (BSs) of HSA for complex formation including Glu-Arg-Asn-Glu-Cys (BS1) and Lys-Glu-Cys-Cys-Glu-Lys (BS2) amino acids. To investigate the interaction of the corresponding binding sites with Fe3+, quantum chemistry calculations were performed at M06-2X/6-31G(d) level in the water. According to density functional theory calculations, binding constant of Fe3+ to human serum albumin in BS1 (log K = 13.33) is lower than that of BS2 (log K = 18.99), showing higher thermodynamic stability of the HSAFe3+ complex in BS2. Natural bond orbital and quantum theory of atoms in molecules analyses demonstrate that the driving force of the complex formation is electrostatic and partially covalent interactions. The results of this research would be valuable to design a suitable iron-chelating agent for the treatment of iron overload.

Holey graphene layers as promising drug delivery systems

Abstract In recent years, two-dimensional drug delivery systems have become some of the most interesting to be studied. A novel two-dimensional layer, denoted by holey graphene (HG), has been recently synthesized using a simple wet-chemical reaction. Motivated by this fascinating finding, in the present study, we have investigated the HG layers as versatile drug delivery systems. The main objective of the present work is to study the interaction of pristine HG as well as boron and nitrogen-doped HG layers with 5-fluorouracil (FU) anticancer drug using the density functional theory (DFT). The Eads of drugs on the considered systems are in the order FU@BHG (−2.40 eV) > FU@BNHG (−1.67 eV) > FU@NHG (−1.01 eV) > FU@HG (−0.83 eV). We found that the more negative value of adsorption energies in the solvent phase reveals that the HG layers can improve their solubility and modify their interaction with the drug in the aqueous phase. Also, our UV–Vis results show that the electronic spectra of the drug/sheet complexes show a blue shift toward lower wavelengths. To gain insight into the binding features of considered systems with FU drug, the Atoms in Molecules analysis was also performed. Our results determine the electrostatic features of the drug/boron-doped HG layers bonding. Therefore, our calculations demonstrated that the HG layers could be used as potential carriers for the delivery of the 5-fluorouracil anticancer drug.

Theoretical study of closo-borate derivatives of general type [BnHn-1COR]2– (n = 6, 10, 12; R = H, CH3, NH2, OH, OCH3) – Borylated analogue of organic carbonyl compounds

This study is focused on the structure, bonding, and reactivity analysis of the derivatives of closo-borate anions [BnHn-1COR]2– (n = 6, 10, 12; R = H, CH3, NH2, OH, OCH3). The phenomena of B–C bonding interactions in the [BnHn-1COR]2– (n = 6, 10, 12; R = H, CH3, NH2, OH, OCH3) have been theoretically studied by using the Quantum Theory of Atoms in Molecules analysis. Several local and integral topological properties of the electron density involved in these interactions have been computed. Also, different chemical reactivity descriptors have been calculated via conceptual density functional theory.

Metal–ring interactions in actinide sandwich compounds: A combined normalized elimination of the small component and local vibrational mode study

The relativistic Hamiltonian Normalised Elimination of the Small Component with atomic unitary transformation (NESCau) was used for the first time to calculate geometries and harmonic vibrational frequencies of actinide sandwich compounds (An: Th, Pa, U, Np, Pu; ). In addition, the Local Vibrational Mode analysis, the Natural Bond Orbital analysis, and the Atoms in Molecules analysis were applied to quantitatively assess the intrinsic strength and the nature of the An-ring interactions. Our results show that actinide sandwich compounds prefer strong covalent interactions between actinide and carbon atoms, similar to those found for homologous ferrocene-type complexes . The metal centre rather than the ring size plays a key role in the strength of those interactions.