Hydrogen bonding versus coordination of adsorbate molecules on Ti-silicalites: a density functional theory study

The present study discusses the results of theoretical calculations obtained at the B3LYP/ 6-31G level on the structural, electronic, and energetic properties of Ti-silicalites. Particularly, the relevance of 5T cluster models, either H- or OH-terminated, in large-scale calculations has been critically considered. It was shown that an open surface structure with one OH group and a closed-bulk structure with no bonded OH group at the Ti site are responsible for the observed UV-vis properties of Ti-silicalite materials. Both water and methanol can preferably interact with Ti-silicalites through the H-bonding mechanism, while ammonia can form either H-bonded or coordination complexes. The calculations support the existence of highly dispersed Ti sites in a tetrahedral environment only in Ti-silicalites because an increase in the coordination number of the Ti site by next-neighbor lattice oxygens is the energetically less favorable process.     

Spectroscopic and density functional studies of the red copper site in nitrosocyanin: role of the protein in determining active site geometric and electronic structure

The electronic structure of the red copper site in nitrosocyanin is defined relative to that of the well understood blue copper site of plastocyanin by using low-temperature absorption, circular dichroism, magnetic circular dichroism, resonance Raman, EPR and X-ray absorption spectroscopies, combined with DFT calculations. These studies indicate that the principal electronic structure change in the red copper site is the sigma rather than the pi donor interaction of the cysteine sulfur with the Cu 3d(x2-y2) redox active molecular orbital (RAMO). Further, MCD data show that there is an increase in ligand field strength due to an increase in coordination number, whereas resonance Raman spectra indicate a weaker Cu-S bond. The latter is supported by the S K-edge data, which demonstrate a less covalent thiolate interaction with the RAMO of nitrosocyanin at 20% relative to plastocyanin at 38%. EXAFS results give a longer Cu-S(Cys) bond distance in nitrosocyanin (2.28 A) compared to plastocyanin (2.08 A) and also show a large change in structure with reduction of the red copper site. The red copper site is the only presently known blue copper-related site with an exogenous water coordinated to the copper. Density functional calculations reproduce the experimental properties and are used to determine the specific protein structure contributions to exogenous ligand binding in red copper. The relative orientation of the CuNNS and the CuSC(beta) planes (determined by the protein sequence) is found to be key in generating an exchangeable coordination position at the red copper active site. The exogenous water ligation at the red copper active site greatly increases the reorganization energy (by approximately 1.0 eV) relative to that of the blue copper protein site, making the red site unfavorable for fast outer-sphere electron transfer, while providing an exchangeable coordination position for inner-sphere electron transfer.     

Outer-sphere effects on reduction potentials of copper sites in proteins: the curious case of high potential type 2 C112D/M121E Pseudomonas aeruginosa azurin

Redox and spectroscopic (electronic absorption, multifrequency electron paramagnetic resonance (EPR), and X-ray absorption) properties together with X-ray crystal structures are reported for the type 2 Cu(II) C112D/M121E variant of Pseudomonas aeruginosa azurin. The results suggest that Cu(II) is constrained from interaction with the proximal glutamate; this structural frustration implies a "rack" mechanism for the 290 mV (vs NHE) reduction potential measured at neutral pH. At high pH (～9), hydrogen bonding in the outer coordination sphere is perturbed to allow axial glutamate ligation to Cu(II), with a decrease in potential to 119 mV. These results highlight the role played by outer-sphere interactions, and the structural constraints they impose, in determining the redox behavior of transition metal protein cofactors.     

The bonding character of AlSO isomers in quartet excited states: Ab initio and density functional theory studies

The geometries and the bonding properties have been predicted for four isomers of AlSO species in the quartet state at density functional theory and coupled cluster [CCSD(T)] all‐electron correlation levels with a large 6‐311+G(3df) basis set. Results have indicated that for the AlSO species in quartet state the lowest state is ⁴A″ state which corresponds to a cyclic structure; the other three isomers (cyclic, bent, and linear) are higher than the lowest state by 26.9 kcal/mol (cyclic ⁴A′), 19.4 kcal/mol (⁴A″), and 28.3 kcal/mol (linear AlSO ⁴Σ), respectively. The calculated dissociation energies for the lowest quartet state species (AlSO: ⁴A″) are 27.3 kcal/mol for the radical mechanism [M(²P)+SO(³Σ^?)] and 154.7 kcal/mol for the mechanism [M(²P)+S(³P)+O(³P)]. Inspection of the bonding character indicates that the cyclic AlSO species in the lowest quartet state (⁴A″) should be classified as thiodioxide (similar to disulfide or dioxide), and the cyclic ⁴A′ state should be classified as thiosuperoxide. The bent Al? SO(⁴A″) species has some thiosuperoxide character, while the linear Al? SO(⁴Σ) structure should be classified as a molecular complex with a weak interaction bonding. However, this thiosuperoxide is not as ionic as LiO₂ and LiSO and is also less ionic than the cyclic AlO₂. In addition, the combinations of Al with SO species exhibit the amphoteric character of Al. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2002     

Modeling halogen bonding with planewave density functional theory: Accuracy and challenges

Inspired by the recent interest of halogen bonding (XB) in the solid state, we detail a comprehensive benchmark study of planewave DFT geometry and interaction energy of lone-pair (LP) type and aromatic (AR) type halogen bonded complexes, using PAW and USPP pseudopotentials. For LP-type XB dimers, PBE-PAW generally agrees with PBE/aug-cc-pVQZ(−pp) geometries but significantly overbinds compared to CCSD(T)/aug-cc-pVQZ(-pp). Grimme's D3 dispersion corrections to PBE-PAW gives better agreement to the MP2/cc-pVTZ(-pp) results for AR-type dimers. For interaction energies, PBE-PAW may overbind or underbind for weaker XBs but clearly overbinds for stronger XBs. D3 dispersion corrections exacerbate the overbinding problem for LP-type complexes but significantly improves agreement for AR-type complexes compared to CCSD(T)/CBS. Finally, for periodic XB crystals, planewave PBE methods slightly underestimate the XB lengths by 0.03 to 0.05 Å. © 2019 Wiley Periodicals, Inc.     

A density functional study of Ce@C82: explanation of the Ce preferential bonding site

Ce has been found experimentally to be preferentially incorporated into the C82 isomer of C2v symmetry as have other lanthanoids in M@C82 (M = La, Pr, Nd, etc.). We have investigated the underlying reason for this preference by calculating structural and electronic properties of Ce@C82 using density functional theory. The ground-state structure of Ce@C82 is found to have the cerium atom attached to the six-membered ring on the C2 axis of the C82-C2v cage, and the encapsulated atom is found to perturb the carbon cage due to chemical bonding. We have found Ce to favor this C2v chemisorption site in C82 by 0.62 eV compared to other positions on the inside wall of the cage. The specific preference of the metal atom to this six-membered ring is explained through electronic structure analysis, which reveals strong hybridization between the d orbitals of cerium and the pi orbitals of the cage that is particularly favorable for this chemisorption site. We propose that this symmetry dictated interaction between the cage and the lanthanide d orbital plays a crucial role when C82 forms in the presence of Ce to produce Ce@C82 and is also more generally applicable for the formation of other lanthanoid M@C82 molecules. Our theoretical computations are the first to explain this well-established fact. Last, the vibrational spectrum of Ce@C82 has been simulated and analyzed to gain insight into the metal-cage vibrations.     

Hybrid density functional theory studies on the magnetic interactions and the weak covalent bonding for the phenalenyl radical dimeric pair

The phenalenyl radical (1) is a prototype of the hydrocarbon radical. Recently, the single crystal of 2,5,8-tri-tert-butylphenalenyl (2) was isolated and showed that the two phenalenyl radicals form a staggered dimeric pair, giving rise to strong antiferromagnetic interactions. The origin of the antiferromagnetic interactions and the nature of the chemical bond for the dimeric pair are challenging issues for chemists. First, spin-polarized hybrid DFT (Becke's half and half LYP (UB2LYP)) and CASSCF calculations were performed for 2 and its simplified model, the staggered-stacking phenalenyl radical dimeric pair (3a), to elucidate the origin of the strong antiferromagnetic coupling and the characteristics of the chemical bond. The calculated results showed that a SOMO-SOMO overlap effect was responsible for the strong antiferromagnetic interactions and weak or intermediate covalent bonding between phenalenyl radicals. The tert-butyl groups introduced at three beta-positions hardly affected the magnetic coupling, mainly causing steric hindrances in the crystalline state. Next, to obtain insight into ferromagnetic stacking, we investigated the stacking effect of staggered (3a)- and eclipsed (3b)-stacking phenalenyl radical dimeric pairs with a change of the SOMO-SOMO overlap on the basis of the extended McConnell model. We found that the stacking mode of the dimeric pair with both a small SOMO-SOMO overlap and a ferromagnetic spin polarization effect provided a ferromagnetic coupling.     

A density functional theory investigation of Fe-N-O bonding in heme proteins and model systems

We report the results of a series of density functional theory (DFT) calculations of the M?ssbauer quadrupole splittings and isomer shifts in NO heme model compounds, together with the results of calculations of the M?ssbauer quadrupole splittings, isomer shifts, and electron paramagnetic resonance hyperfine coupling constants in a model Fe(II)(NO)(imidazole) complex as a function of Fe-NO bond length and Fe-N-O bond angle. The results of the M?ssbauer quadrupole splitting and isomer shift calculations on the NO heme model compounds show good accord between theory and experiment, with the largest errors being observed for structures having the largest crystallographic R(1) values. The results of the property surface calculations were then used to calculate Fe-NO bond length and Fe-N-O bond angle probability surfaces (Z-surfaces) for a nitrosyl hemoglobin, using, in addition, an energy filter. The results obtained yielded a most probable Fe-NO bond length (r) of 1.79 A and an Fe-N-O bond angle (beta) of 136 degrees -137 degrees. This bond length is somewhat longer than those observed in most model compounds but may be due, at least in part, to hydrogen bond formation with the distal His residue. Bond elongation was also observed in a geometry optimized Fe(II)(NO)(imidazole) complex hydrogen bonded to an imidazole residue, in which we find r = 1.76-1.78 A and beta = 137 degrees -138 degrees. The computed bond angles are close to the canonical approximately 140 degrees value found in most model systems. Highly bent Fe-N-O bond angles or very long Fe-NO bond lengths seem unlikely to occur in proteins, due to their high energies. We also investigated the molecular orbitals and spin densities in each of the six coordinate systems investigated and found the orbitals and spin densities to be generally similar those described previously for five coordinate systems. Taken together, these results show that M?ssbauer quadrupole splittings and isomer shifts, in addition to electron paramagnetic resonance hyperfine coupling constants, can now be calculated for nitrosyl heme systems with relatively good accuracy and that the results so obtained can be used to determine Fe-N-O geometries in metalloproteins. The Z-surface approach is thus applicable to both diamagnetic (CO) and paramagnetic (NO) heme proteins with in both cases the metal-ligand binding geometries found in the proteins being very close to those seen in model systems.     

Investigation of the metal binding site in methionine aminopeptidase by density functional theory

All methionine aminopeptidases exhibit the same conserved metal binding site. The structure of this site with either Co²⁺ions or Zn²⁺ions was investigated using density functional theory. The calculations showed that the structure of the site was not influenced by the identity of the metal ions. This was the case for both of the systems studied; one based on the X-ray structure of the human methionine aminopeptidase type 2 (hMetAP-2) and the other based on the X-ray structure of the E. colimethionine aminopeptidase type 1 (eMetAP-1). Another important structural issue is the identity of the bridging oxygen, which is part of either a water molecule or a hydroxide ion. Within the site of hMetAP-2 the results strongly indicate that a hydroxide ion bridges the metal ions. By contrast, the nature of the oxygen bridging the metal ions within the metal binding site of eMetAP-1 cannot be determined based on the results here, due to the similar structural results obtained with a bridging water molecule and a bridging hydroxide ion.     

Vibrational spectroscopic and density functional theory studies of chloranil-imidazole interaction

The present work reports vibrational spectra and density functional theory calculations for chloranil, imidazole and their complexes. The experimentally observed infrared and Raman bands have been assigned with the help of calculated vibrational frequencies and potential energy distribution analysis. Some bands of chloranil and imidazole have been found to shift on the complex formation due to partial electronic charge transfer from imidazole to chloranil. The charge transfer between these molecules is also corroborated by the electronic absorption spectroscopy and calculations. The theoretical values of the interaction energy of various possible chloranil-imidazole interactions suggest that the two molecules interact preferably via N and H atoms of imidazole and CO group of chloranil with their molecular planes almost perpendicular to each other.     

Equilibrium adsorption in cylindrical mesopores: a modified Broekhoff and de Boer theory versus density functional theory

This paper presents a thermodynamic analysis of capillary condensation phenomena in cylindrical pores. Here, we modified the Broekhoff and de Boer (BdB) model for cylindrical pores accounting for the effect of the pore radius on the potential exerted by the pore walls. The new approach incorporates the recently published standard nitrogen and argon adsorption isotherm on nonporous silica LiChrospher Si-1000. The developed model is tested against the nonlocal density functional theory (NLDFT), and the criterion for this comparison is the condensation/evaporation pressure versus the pore diameter. The quantitative agreement between the NLDFT and the refined version of the BdB theory is ascertained for pores larger than 2 nm. The modified BdB theory was applied to the experimental adsorption branch of adsorption isotherms of a number of MCM-41 samples to determine their pore size distributions (PSDs). It was found that the PSDs determined with the new BdB approach coincide with those determined with the NLDFT (also using the experimental adsorption branch). As opposed to the NLDFT, the modified BdB theory is very simple in its utilization and therefore can be used as a convenient tool to obtain PSDs of all mesoporous solids from the analysis of the adsorption branch of adsorption isotherms of any subcritical fluids.     

Effect of metal complex formation on the antibacterial activity of nitazoxanide: Spectroscopic and density functional theory calculations

In the present work, experimental and theoretical structural studies of two new nitazoxanide (NTZ) complexes, [Co(NTZ)(NO₃)₂(OH₂)] ( 1 ) and [Ni(NTZ)(CH₃COO)(OH₂)]·CH₃COO ( 2 ) were reported. The susceptibility of Staphylococcus aureus and Escherichia coli towards NTZ and its complexes was assessed. NTZ behaves as a monodentate ligand via the thiazole N atom forming distorted octahedral and tetrahedral complexes with Co(II) and Ni(II) ions, respectively. The d‐d transitions were assigned by the aid of time‐dependent density functional theory calculations. The magnetic susceptibility value of 1 remains unchanged in the temperature range of 298–77K, while that of 2 decreases linearly with the temperature to attain 2.79 μ_B at 77K. Coordination of NTZ (0.084 μmol ml^?1) to Co(II) ( 1 ) (0.028 μmol ml^?1) and Ni(II) ions ( 2 ) (0.079 μmol ml^?1) leads to an improvement in the toxicity against S. aureus.     

An ab initio and density functional theory study of the structure and bonding of sulfur ylides

Sulfur ylides are useful synthetic intermediates that are formed from the interaction between singlet carbenes and sulfur-containing molecules. Partial double-bond character frequently has been proposed as a key contributor to the stability of sulfur ylides. Calculations at the B3LYP, MP2, and CCSD(T) levels of theory employing various basis sets have been performed on the sulfur ylides H(2)S-CH(2) and (CH(3))(2)S-CH(2) in order to investigate the structure and bonding of these systems. The following general properties of sulfur ylides were observed from the computational studies: C-S bond distances that are close in length to that of a typical C-S double bond, high charge transfer from the sulfide to the carbene, and large torsional rotation barriers. Analysis of the sulfur ylide charge distribution indicates that the unusually short C-S bond distance can be attributed in part to the electrostatic attraction between highly oppositely charged carbon and sulfur atoms. Furthermore, n --> sigma* stabilization arising from donation of electron density from the carbon lone pair orbital into S-H or S-C antibonding orbitals leads to larger than expected torsional barriers. Finally, natural resonance theory analysis indicates that the bond order of the sulfur ylides H(2)S-CH(2) and (CH(3))(2)S-CH(2) is 1.4-1.5, intermediate between a single and double bond.     

Hydrogen bonding affects the [NiFe] active site of Desulfovibrio vulgaris Miyazaki F hydrogenase: a hyperfine sublevel correlation spectroscopy and density functional theory study

Pulse electron paramagnetic resonance and hyperfine sublevel correlation spectroscopy have been used to investigate nitrogen coordination of the active site of [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F in its oxidized "ready" state. The obtained (14)N hyperfine (A = [+1.32, +1.32, +2.07] MHz) and nuclear quadrupole (e(2)qQ/h = -1.9 MHz, eta = 0.37) coupling constants were assigned to the N(epsilon) of a highly conserved histidine (His88) by studying a hydrogenase preparation in which the histidines were (15)N labeled. The histidine is hydrogen-bonded via its N(epsilon)-H to the nickel-coordinating sulfur of a cysteine (Cys549) that carries an appreciable amount of spin density. Through the hydrogen bond a small fraction of the spin density ( approximately 1%) is delocalized onto the histidine ring giving rise to an isotropic (14)N hyperfine coupling constant of about 1.6 MHz. These conclusions are supported by density functional calculations. The measured (14)N quadrupole coupling constants are related to the polarization of the N(epsilon)-H bond, and the respective hydrogen bond can be classified as being weak.     

Structural, electronic, and bonding properties of zeolite Sn-beta: a periodic density functional theory study

The structural, electronic, and the bonding properties of the zeolite Sn-beta (Sn-BEA) have been investigated by using the periodic density functional theory. Each of the nine different T-sites in BEA were substituted by Sn atoms and all the nine geometries were completely optimized by using the plane-wave basis set in conjunction with the ultra-soft pseudopotential. On the basis of the structural and the electronic properties, it has been demonstrated that the substitution of Sn atoms in the BEA framework is an endothermic process and hence the incorporation of Sn in the BEA is limited. The lowest unoccupied molecular orbitals (LUMO) energies have been used to characterize the Lewis acidity of each T-site. On the basis of the relative cohesive energy and the LUMO energy, the T2 site is shown to be the most favorable site for the substitution Sn atoms in the BEA framework.     

Spectroscopic and density functional theory studies of the molecular geometry and electronic structure of classical and nonclassical radical ions derived from 7-benzhydrylidenenorbornene analogues

A spectroscopic study, using nanosecond time-resolved laser flash photolysis and gamma-irradiation of low-temperature matrices, was undertaken along with a theoretical study using density functional theory (DFT) and time-dependent (TD)-DFT calculations to gain insight into the molecular geometry and electronic structure of radical cations and radical anions of 7-benzhydrylidenenorbornene (4) and its derivatives 6-8. The radical ions 4(.+), 6(.+), 7(.+), 8(.+), 4(.-), 6(.-), 7(.-), and 8(.-) exhibited clear absorption bands in the 350-800 nm region, which were reproduced successfully from the electronic transitions calculated with TD-UB3LYP/cc-pVDZ. Radical cations 4(.+) and 8(.+) are consistent with a bent structure having a delocalized electronic state where the spin and charge are delocalized not only in the benzhydrylidene subunit but also in the residual subunit. In contrast, 6(.+) and 7(.+) have nonbent structures with a localized electronic state where their spin and charge are localized in the benzhydrylidene subunit only. Therefore, 4(.+) and 89(.+) have a nonclassical nature, with 6(.+) and 7(.+) possessing a classical nature. In contrast, in the radical anion system, 7(.-) and 8(.-) are considered nonclassical, and 4(.-) and 6(.-) are classical. Orbital interaction theory and DFT calculations can account fully for the spectroscopic features, molecular geometries, and electronic structures of the radical ions. For example, the shift of the absorption bands and the nonclassical nature of 4(.+) are due to the antibonding character of the highest occupied molecular orbital (HOMO) of 4, and those of 7(.-) arise from the bonding character of the lowest unoccupied molecular orbital (LUMO) of 7. A topological agreement of p-orbitals at C-2, C-3 (or C-5, C-6), and C-7 produces strong electronic coupling with an antibonding or a bonding character in the frontier orbitals. It is the ethylene and butadiene skeleton at C-2-C-3 (or C-5-C-6), with its contrasting topology in the HOMO and LUMO of the neutral precursor, that holds the key to deducing the nonclassical nature of the 7-benzhydrylidenenorbornene-type radical cation and radical anion systems.     

Gadolinium ion bonding on the surface of carboxylated detonation nanodiamond in terms of magnetochemistry and density functional theory

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Magic number silicon dioxide-based clusters: laser ablation-mass spectrometric and density functional theory studies

The magic number silica clusters [(SiO(2))(n)O(2)H(3)](-) with n = 4 and 8 have been observed in the XeCl excimer laser (308 nm) ablation of various porous siliceous materials. The structural origin of the magic number clusters has been studied by the density functional theoretical calculation at the B3LYP/6-31G** level, with a genetic algorithm as a supplementary tool for global structure searching. The DFT results of the first magic number cluster are parallel to the corresponding Hartree-Fock results previously reported with only small differences in the structural parameters. Theoretical calculation predicts that the first magic number cluster (SiO(2))(4)O(2)H(4) and its anion [(SiO(2))(4)O(2)H(3)](-) will most probably take pseudotetrahedral cage-like structures. To study the structural properties of the second magic number cluster, geometries of the bare cluster (SiO(2))(8), the neutral complex cluster (SiO(2))(8)O(2)H(4), and the anionic cluster [(SiO(2))(8)O(2)H(3)](-) are fully optimized at the B3LYP/6-31G** level, and the corresponding vibrational frequencies are calculated. The DFT calculations predict that the ground state of the bare silica octamer (SiO(2))(8) has a linear chain structure, whereas the second magic number complex cluster (SiO(2))(8)O(2)H(4) and its anion [(SiO(2))(8)O(2)H(3)](-) are most probably a mixture of cubic cage-like structural isomers with an O atom inside the cage and several quasi-bicage isomers with high intercage interactions. The stabilization of these structures can also be attributed to the active participation of the group of atoms 2O and 4H (3H for the anion) in chemical bonding during cluster formation. Our theoretical calculation gives preliminary structural interpretation of the presence of the first and second magic number clusters and the absence of higher magic numbers.     

Multicoefficient extrapolated density functional theory studies of pi...pi interactions: the benzene dimer

We report tests of new (2005) and established (1999-2003) multilevel methods against essentially converged benchmark results for nonbonded interactions in benzene dimers. We found that the newly developed multicoefficient extrapolated density functional theory (DFT) methods (which combine DFT with correlated wave function methods) give better performance than multilevel methods such as G3SX, G3SX(MP3), and CBS-QB3 that are based purely on wave function theory (WFT); furthermore, they have a lower computational cost. We conclude that our empirical approach for combining WFT methods with DFT methods is a very efficient and effective way for describing not only covalent interactions (as shown previously) but also nonbonded interactions.