Optimized Bond Distances Research Articles

Antimony stable isotope fractionation during adsorption onto birnessite: A molecular perspective from X-ray absorption spectroscopy and density functional theory

Sorption of antimony (Sb) onto birnessite significantly influences the fate of Sb in oceanic and terrestrial environments and fractionates Sb isotopes. Nevertheless, little is known about Sb isotopic fractionation during its adsorption on birnessite. Here, we show the value of Δ123Sbadsorbed-aqueous increases from −0.398 to −0.332 ‰ in 1 h and then decreases and stabilizes at −0.384 ‰ in 72 h. The enrichment of the light Sb isotope is predominantly due to the distortion of the octahedral symmetry. X-ray absorption spectroscopy results indicate Sb first forms a double-corner-sharing complex on birnessite and then transforms to a double-edge-sharing complex during adsorption. The optimized bond distances for double-corner-sharing (3.37 Å) and double-edge-sharing (2.90 Å) complexes calculated using density functional theory (DFT) fits well with the structure (3.41 and 3.00 Å) revealed by X-ray absorption spectroscopy, respectively. The fractionation derived from reduced partition function ratios calculated using DFT aligns well with the experimental results. Therefore, the variation in Sb isotopic fractionation during adsorption is attributed to the evolving structure of Sb complexes on birnessite. Our results demonstrate the isotopic fractionation of Sb during adsorption on birnessite and provide a molecular-scale understanding of Sb behavior, contributing to the correct reconstruction of the Sb isotope composition of ancient seawater using ferromanganese crusts and nodules, and efforts to trace Sb migration in epigenetic mining environments.

Theoretical Modeling of B12N12 Nanocage for the Effective Removal of Paracetamol from Drinking Water

In our current investigation, we employed a B12N12 nanocage to extract paracetamol from water utilizing a DFT approach. We explored three distinct positions of paracetamol concerning its interaction with the B12N12 nanocage, designated as complex-1 (BNP-1), complex-2 (BNP-2), and complex-3 (BNP-3), under both aqueous and gaseous conditions. The optimized bond distances exhibited strong interactions between the nanocage and the paracetamol drug in BNP-1 and BNP-3. Notably, BNP-1 and BNP-3 displayed substantial chemisorption energies, measuring at −27.94 and −15.31 kcal/mol in the gas phase and −30.69 and −15.60 kcal/mol in the aqueous medium, respectively. In contrast, BNP-2 displayed a physiosorbed nature, indicating weaker interactions with values of −6.97 kcal/mol in the gas phase and −4.98 kcal/mol in the aqueous medium. Our analysis of charge transfer revealed significant charge transfer between the B12N12 nanocage and paracetamol. Additionally, a Quantum Theory of Atoms in Molecules (QTAIM) analysis confirmed that the O─B bond within BNP-1 and BNP-3 exhibited a strong covalent and partial bond, encompassing both covalent and electrostatic interactions. In contrast, the H─N bond within BNP-2 displayed a weaker hydrogen bond. Further investigation through Noncovalent Interaction (NCI) and Reduced Density Gradient (RDG) analyses reinforced the presence of strong interactions in BNP-1 and BNP-3, while indicating weaker interactions in BNP-2. The decrease in the electronic band gap (Eg) demonstrated the potential of B12N12 as a promising adsorbent for paracetamol. Examining thermodynamics, the negative values of ∆H (enthalpy change) and ∆G (Gibbs free energy change) pointed out the exothermic and spontaneous nature of the adsorption process. Overall, our study underscores the potential of B12N12 as an effective adsorbent for eliminating paracetamol from wastewater.

Theoretical insight of ciprofloxacin removal from water using boron nitride (B12N12) nanocage

In the present study we used B12N12 nanocage for the removal of ciprofloxacin (CIP) from water using DFT approach. Three positions of CIP are considered for the interaction with B12N12 nanocage i.e. complex-1 (CMP-1), complex-2 (CMP-2) and complex-3 (CMP-3) in aqueous and gas phase. The optimized bond distances show that CMP-1 and CMP-2 interacts strongly with the nanocage. The adsorption energies (Ead) reveal that the CMP-1 and CMP-2 are chemisorbed having -26.83 and -24.67 kcal/mol in gas phase and -24.34 and-22.88 kcal/mol in aqueous medium while complex-3 (CMP-3) physisorbed having -8.94 kcal/mol in gas phase and -8.40 kcal/mol in aqueous medium. The charge transfer analysis shows significant charge transfer between adsorbate and adsorbent. The atoms in molecule analysis (AIM) also confirm that OHN bond in CMP-1 is strong hydrogen bond while the O—B bond in CMP-1 and CMP-2 is a covalent bond. Non covalent interactions (NCI) and reduced density gradient (RDG) analyses also show the presence of strong interactions between adsorbate and adsorbent. Energy decomposition analysis (EDA) analysis suggests that electrostatic (ES) energy has a larger contribution to the total interaction energy compared to exchange (EX), dispersion (DISP) and induction (IND) energy in all complexes showing maximum overlap of orbitals demonstrating strong interactions. Variations in electronic band gap (Egap) show that B12N12 is a potential adsorbent for CIP. The negative values of ∆H and ∆G suggests the exothermic, chemisorption and spontaneous nature of adsorption process. The overall study shows that B12N12 may be a better adsorbent for the adsorption of CIP.

Rare-Earth Metal Boroxide with Formal Triple Metal–Oxygen Orbital Interaction: Synthesis from B(C 6 F 5 ) 3 ·H 2 O and Radical-Anion Ligated Rare-Earth Metal Amides

Rare-earth metal boroxides are not only rare and of great synthetic challenge but also important theoretically due to their unrevealed bonding characteristics. In this paper, we report the synthesi...

Prediction of Bond Dissociation Energies/Heats of Formation for Diatomic Transition Metal Compounds: CCSD(T) Works.

It was recently reported ( J. Chem. Theory Comput. 2015 , 11 , 2036 - 2052 ) that the coupled cluster singles and doubles with perturbative triples method, CCSD(T), should not be used as a benchmark tool for the prediction of dissociation energies (heats of formation) for the first row transition metal diatomics based on a comparison with the experimental thermodynamic values for a set of 20 diatomics. In the present work the bond dissociation energies as well as the heats of formation for those diatomics have been calculated by the Feller-Peterson-Dixon approach at the CCSD(T)/complete basis set (CBS) level of theory including scalar relativistic corrections and correlation of the outer shell of core electrons in addition to the valence electrons. Revised experimental values for the hydrides are presented that are based on new heterolytic R-H bond dissociation energies, which are needed for analysis of the mass spectrometry experiments. The agreement between the calculated bond dissociation energies and the revised experimental values of the hydrides is good. Good agreement of the calculated bond dissociation energies/heats of formation is also found for most of the chlorides, oxides, and sulfides given the experimental error bars from experiment and those of the transition metal atoms in the gas phase. Thus, reliable results can be achieved by the CCSD(T) method at the CBS limit. The use of PW91 orbitals for the CCSD(T) calculations improves the predictions for some compounds with large T1 diagnostics at the HF-CCSD(T) level. The optimized bond distances and calculated vibrational frequencies for the diatomics also agree well with the available experimental values.

A Theoretical Investigation of the Structural, Spectroscopic and Optical Properties of Adenine

The structural, spectroscopic (IR, NMR and UVis) UV-Vis) and optical properties of adenine (6-aminopurine, C5H5N5) are investigated theoretically using HF/DFT hybrid approach B3LYP. The calculated results are compared with available experimental data. The optimized bond distances and bond angles are converged within ±0.01 Å and ±0.8° with respect to the experimental values. The investigation of1H NMR chemical shift spectra of the aromatic C-H protons shows that the maximum deviation of the calculated chemical shift is ~ 0.53 ppm compared to the experimental data. The calculated vibrational spectra analysis shows four distinct IR active mode of vibrations which are assigned as scissoring vibration of –NH2, symmetric stretching vibration of, –NH2, free –NH vibration and anti-symmetric stretching vibration of–NH2, respectively The electronic and optical properties are calculated by Time Dependent Density Functional Theory (TD-DFT) approach. A reasonable agreement is obtained for the calculated optical absorption energy with the experimental value. Dhaka Univ. J. Sci. 64(1): 77-81, 2016 (January)

Synthesis, crystal structures and theoretical studies of dinuclear Mn(II) and Ni(II) complexes of phenol-based “end-off” compartmental ligand

Two novel complexes [Mn2(phmp)2](ClO4)2 (1) and [Ni2(phmp)(μ-H2O)(H2O)4](NO3)3 (2) were synthesized using an “end-off” compartmental ligand [H-phmp = 4-Methyl-2,6-bis-(pyridin-2-yl-hydrazonomethyl)-phenol] with Mn(II)-perchlorate and Ni(II)-nitrate salts as metal precursors. Both these complexes were characterized by spectroscopic (IR, UV–Vis) and X-ray crystal structure analysis. The ligand, H-phmp acts as a pentadentate NNONN donor for both the metal complexes and the geometry of the complexes 1 and 2 is distorted octahedral. The DFT optimized bond distances and angles are well correlate to the X-ray structure bond parameters. For complex 1 the transitions at 435 nm and 428 nm have mixed MLCT (dπ(Mn) → π*(L)) and ILCT (π(L) → π*(L)) character whereas other transitions correspond to intra-ligand charge transfer transitions (ILCT). For complex 2, weak transitions at 464 and 405 nm correspond to ligand to metal charge transfer transitions (LMCT) (π(L) → dπ(Ni)) and most of the other transitions have ILCT character. As anticipated, various weak forces, i.e. anion–π/π–anion/anion–π/π–NH interactions as well as C–H/π interaction, play a key role in stabilizing the self-assembly process observed for both compounds.

Relativistic effects for the reaction Sg + 6 CO → Sg(CO)6: Prediction of the mean bond energy, atomization energy, and existence of the first organometallic transactinide superheavy hexacarbonyl Sg(CO)6.

Our ab initio all-electron fully relativistic Dirac-Fock (DF) and nonrelativistic (NR) Hartree-Fock calculations predict the DF relativistic and NR energies for the reaction: Sg + 6 CO → Sg(CO)6 as -7.39 and -6.96 eV, respectively, i.e., our calculated ground state total DF relativistic and NR energies for the reaction product Sg(CO)6 are lower by 7.39 and 6.96 eV than the total DF and NR ground state energies of the reactants, viz., one Sg atom plus six CO molecules, respectively. Our calculated DF relativistic and NR atomization energies (Ae) are 65.23 and 64.82 eV, respectively, and so the contribution of relativistic effects to the Ae of ∼0.40 eV is marginal. The Sg-C and C-O optimized bond distances for the octahedral geometry as calculated in our DF (NR) calculations are 2.151 (2.318 Å) and 1.119 (1.114 Å), respectively. The BSSE correction calculated using the DIRAC code ∼14 kcal/mol. The relativistic DF and NR mean energies predicted by us are 118.8 and 111.9 kJ/mol, respectively, and the contribution of ∼7 kJ/mol due to relativistic effects to the mean energy of Sg(CO)6 is negligible. Ours are the first calculations of the relativistic effects for the atomization energy, mean bond energy, and energy of the reaction for possible formation of Sg(CO)6, and both our relativistic DF and the NR treatments clearly predict for the first time the existence of hexacarbonyl of the transactinide superheavy element seaborgium Sg. In conclusion, relativistic effects are not significant for Sg(CO)6.

Structure and bonding analysis of intermediate model heme-imidazole and heme-thiolate enzymes complexed with formate, acetate and nitrate: A theoretical study

Structure and bonding analysis of the FeO bonds in the model heme-imidazole and heme-thiolate complexes [(por)Fe(Im)(R)] (R=HC(O)O−, 1FeIm, R=H3CC(O)O−, 2FeIm, R=NO3−, 3FeIm) and [(por)Fe(SMe))(R)]− (R=HC(O)O−, 4FeSMe, R=H3CC(O)O−, 5FeSMe, R=NO3−, 6FeSMe) were investigated at the DFT/TZP level of theory using density functionals BP86, PW91, PBE, TPSS and B3LYP. The FeO bond distances at BP86/TZP in the complexes [(por)Fe(Im)(R)] (1.858Å in 1FeIm, 1.868Å in 2FeIm and 1.919Å in 3FeIm) and [(por)Fe(SMe)(R)]− (1.955Å in 4FeSMe, 1.981Å in 5FeSMe and 1.991Å in 6FeSMe) are longer than those expected for a FeO single bond estimated on the basis of covalent radii predictions (FeO=1.79Å). The FeO bond distances in [(por)Fe(Im)(R)] 1FeIm–3FeIm are shorter than those in [(por)Fe(SMe)(R)]−4FeSMe–6FeSMe. The thiolate is more trans-directing ligand than the imidazole ligand. The results of optimized geometries, NPA charges, Wiberg bond indices, NHO analysis and BDEs clearly indicate that the formate, acetate and nitrate ligands bind more weakly in heme-thiolate complexes than in heme-imidazole complexes. The reaction intermediate of chloroperoxidase enzyme would be more reactive with organic substrates than the myeloperoxidase (MPO) enzyme. The quartet and the sextet spin states are less stable than the doublet spin state. The optimized bond distances are shortest for doublet spin state.

Synthesis and ECL performance of highly efficient bimetallic ruthenium tris-bipyridyl complexes

In order to find the ideal carbon chain linkage number n for achieving the highest ECL in bimetallic ruthenium tris-bipyridyl complexes, a series of novel complexes [(bpy)(2)Ru(bpy')(CH(2))(n)(bpy')Ru(bpy)(2)](4+) (, where bpy is 2,2'-bipyridyl, n = 10, 12, 14) for a coreactant electrochemiluminescence (ECL) system have been synthesized. Their ECL properties at a Au electrode have been studied in 0.1 M phosphate buffer by using tripropylamine (TPrA), 2-(dibutylamino)ethanol (DBAE) and melamine as the coreactant, to compare with that of the previously reported bimetallic ruthenium analogous complex [(bpy)(2)Ru(bpy')(CH(2))(8)(bpy')Ru(bpy)(2)](4+). The results demonstrate that the ECL intensity depends largely on the length of the saturated carbon chain linkage number n. The highest ECL is reached when n = 10, suggesting that a synergistic effect on ECL enhancement co-exists between the two intramolecular linked ruthenium activating centers. Density functional theory (DFT) calculation demonstrated that the optimized bond distances between Ru and N(bpy') are the longest both in the ground and the excited triplet states in the case of n = 10, while those for Ru and N(bpy) are the shortest in the excited triplet states. All these factors may be responsible for the above mentioned results. This study provided a methodology to further improve and tune ECL efficiency by using bimetallic ruthenium complexes linked by a flexible saturated carbon chain.

A DFT study of N-doped AlP nanotubes

We performed density functional theory calculations for nitrogen-doped models of the representative structures of (6,0) zigzag and (4,4) armchair aluminum phosphide nanotubes (AlPNTs). Our results indicate that the optimized bond distances and tip diameters do not detect the effects of the N-doped regions; however, the effects are observed for the band gap energies and dipole moments. It is noted that substitution of the P atom by the N atom does not influence the value of band gap energy for this N-doped model. The results also indicate that the tendency of the Al atom for contribution to the Al–N bond is stronger than the tendency of the P atom for contribution to the N–P bond; therefore, the latter form of substitution makes the AlPNTs interesting as reactive materials towards other atoms or molecules, especially for the the zigzag AlPNT.

A transient form of 2-aza-21-carbaporphyrin prearranged for fusion: DFT studies

The formation mechanism of the fused porphyrin (CTPPH-NF) involves a rotation of the N(2) pyrrole ring of 2-aza-21-carba-5,10,15,20-tetraarylporphyrin (CTPPH2) which is subsequently followed by formation of the C(3)–N(24) bond to yield the macrocycle with the fused pyrrole tripentacyclic ring. To approach the problem of the relative stability of the prearranged transient species theoretical investigations have been performed applying density functional theory (DFT). The molecular structures and electronic energy have been studied for idealized 2-aza-21-carbaporphyrin (CPPH2) and porphyrin (PH2) macrocycles created by a replacement of phenyl or other substituents with hydrogen or methyl groups. The following forms of 2-aza-21-carbaporphyrin and porphyrin were studied: CPH2-I, 2-NH-CPH-I and PH2-I in relation to CPH2-P, 2-NH-CPH-P and PH2-P, respectively (P indicates regular geometry (N(21) or C(21) located in the inner perimeter) and I indicates inverted geometry (N(21) or C(21) located in the outer perimeter). A π delocalization exists through the inverted macrocycles: PH2-I, CPH2-I and 2-NH-CPH-I. The B3LYP/6-31G** optimized bond distances of I macrocycles reproduce the pattern of the P counterparts. The B3LYP/6-31G**//B3LYP/6-31G** calculated energy differences between the P and I structures are very similar for two considered 2-aza-21-carbaporphyrin tautomers: CPH 2-P → CPH 2-I, 18.50 kcal mol-1, 2- NH - CPH -P → 2- NH - CPH -I, 17.55 kcal mol-1; but essentially different for the regular porphyrin PH2-P → PH 2-I, 45.56 kcal mol-1. The methyl substitution at the 21-carbon or 5 and 20 meso positions preserved the order of stability as the calculated energy differences equal 21- CH 3- CPH 2-P → 21- CH 3- CPH 2-I, 13.39 kcal mol-1; 5,20- CH 3- CPH 2-P → 5,20- CH 3- CPH 2-I, 17.87 kcal mol-1.

Geometry and Tautomerism of 26,28-Dioxasapphyrin and 26,28-Dithiasapphyrin: DFT Studies

The density functional theory (DFT) calculations have been carried out on 26,28-dioxasapphyrin (O2SapH) and 26,28-dithiasapphyrin (S2SapH) including all likely geometrical isomers and NH tautomers. The peculiar skeleton of sapphyrin with an inverted pyrrole ring lying opposite to the bipyrrolic unit (I) and the regular planar arrangement (P) of the macrocycle with three nitrogens and two heteroatoms pointing to the center of the macrocycle were considered. Consequently, a total of eight structures resulting from the feasible geometrical isomerism and NH tautomerism of diheterosapphyrins were studied. The optimized bond distances and angles of 26,28-diheterosapphyrins compare favorably with the relevant X-ray structures of sapphyrins and heterosapphyrin. The pyrrole bond distances decrease in the series: Cα−Cβ > Cα−Cmeso > Cα−N > Cβ−Cβ, reproducing the pattern of the regular porphyrin or dicationic sapphyrins. There is an appreciable effect from the aromatic character of the macrocycle on the furan or thi...

Theoretical study of N 28 molecule using semiempirical MO methods

The N 28 cluster type molecule with T d point group has been studied for the first time. Two reliable semiempirical methods, PM3 and AM1, were applied in this theoretical study. Geometrical optimization, vibrational frequencies and thermal chemical calculations are reported and all the results indicate that N 28 is a stable molecule. Three kinds of nitrogen atom and three types of NN bond are identified in this T d structure. A comparison of the optimized bond distances, first ionization potentials and the average bond energies between N 28 and N 20 showed that the structural behavior of these two cluster type molecules is quite similar. Both belong to the category of stable high energy compounds.

Theoretical study of the N 20 molecule

In the study of the N 20 molecule with an I h symmetry group, the following methods were applied: 6-31G, 3-21G and STO-3G ab initio and PM3 semiempirical MO methods. Both geometrical optimization and frequency calculations are reported. Results of optimized bond distances ( d N N ), first ionization potential, ΔH a , ΔG a and bond energy, for the cases of 6-31G, 3-21G, and PM3 showed that the N 20 molecule is a highly stable compound with a delocalized NN single bonded cluster structure.

Organometallic Analogs of the Diels-Alder Reaction: Molybdenum Dimer + Ethylene; Molybdenum Dimer + Butadiene

A theoretical study of the symmetry-concerted Diels-Alder analogue reactions of Mo{sub 2} with 1,3-butadiene and ethylene is presented. Structure optimizations indicated elongation of the Mo-Mo and C{double_bond}C bonds in the complexes. The optimized bond distances were found to be close to one known in organomolybdenum complexes. The presented potential surfaces indicated, in agreement with symmetry-concerted models, that the Mo{sub 2}-Eth complex formation is thermally forbidden, as the reaction has to proceed in the excited state, but the Mo{sub 2}-But complex may be formed in the ground state with addition of thermal energy.

Comparison between ab Initio and Modified INDO‐MO Calculations of N20

AbstractBoth STO‐3G ab initio and s‐p separation‐type‐modified INDO semiempirical methods were applied to molecular‐orbital calculation of the N20 molecule. From these two methods, the optimized bond distances between the nearest N atoms (dn‐n) and the most calculated thermodynamic data are close to each other. The positive values of ΔHa° and ΔGa° for the atomization reaction in this work prove that N20 is stable. In contrast to conventional INDO and MINDO/3, but similar to former AMI and MNDO calculations, both ΔHr° and ΔGr° are positive in the formation reaction, which indicates that N20 belongs to the category of high‐energy molecules.

Molecular orbital studies of the spectral and structural properties of chlorosilylidyne, SiCl

Si-Cl bond distances for the X̃ 2 Π ground and low lying b̃ 4 Σ, Ã 2 Σ and B̃' 2 Δ excited states of SiCl have been optimized at the SCF and CI level with 6–31G ★ basis set. Optimized bond distances are in good agreement with experimental values. Computed electronic excitation energies for the X̃ 2Π-Ã 2Σ and X̃ 2Π-B̃' 2 Δ transitions compare well with the observed spectrum. The calculated harmonic vibrational frequency for the ground state, 525.2 cm −1, also agrees with the experimental value 535.6 cm −1.