Partial Covalent Interaction Research Articles

Combined experimental and theoretical studies of some uranium(VI) complexes derived from imidazole-based carbenes

A series of bidentate, viz., 1,1'-(1,2-ethylene)-3,3'-dimethyldiimidazoline-2,2'-diylidene (L1), 1-methyl-3-(2-pyridylmethyl)-imidazoline-2-ylidene (L2) and tridentate, viz., 1,3-bis(2-pyridyl)-imidazoline-2-ylidene (L3) ligands have been obtained from their corresponding imidazolium salts through deprotonation reactions. Treatment of UO2Cl2(THF)3 with one equivalent L3 produces air-stable U(VI)-carbene complex 3, characterized by elemental analysis, FTIR, NMR spectroscopy as well as extended X-ray absorption fine structure (EXAFS) analysis. EXAFS result indicates that the ligand is bonded through one C and two N-atoms to the uranium atom. Attempts to synthesize uranyl complexes derived from L1 and L2 were also successful but these complexes are decomposed quickly within one hour at room temperature. 3 produces pure UO2 powder when heated under an argon atmosphere from room temperature to 600 °C with constant heating rate of 5 °C/min. The solid-state UV–Vis spectrum of the compound shows absorption peaks at 332 and 450 nm. The excitation spectrum of 3 (at λ em = 520 nm) exhibits two almost symmetrical peaks at 273 and 368 nm. Density functional theory-based quantum mechanical calculations indicate that a partial covalent interaction exists between the carbene C and U while a weak non-covalent interaction exists between carbene N and U atoms.

Phosphorus-doped T-graphene nanocapsule toward O3 and SO2 gas sensing: a DFT and QTAIM analysis

Tetragonal graphene nano-capsule (TGC), a novel stable carbon allotrope of sp2 hybridization is designed and doped with phosphorus (P) to study the O3 and SO2 gas sensitivity via density functional theory calculation. Real frequencies verified the natural existence of both TGC and P-doped TGC (PTGC). Both TGC and PTGC suffer structural deformations due to interaction with O3 and SO2 gases. The amount of charge transfer from the adsorbent to the gas molecule is significantly greater for O3 adsorption than SO2 adsorption. The adsorption energies for TGC + O3 and PTGC + O3 complexes are − 3.46 and − 4.34 eV respectively, whereas for TGC + SO2 and PTGC + SO2 complexes the value decreased to − 0.29 and − 0.30 eV respectively. The dissociation of O3 is observed via interaction with PTGC. A significant variation in electronic energy gap and conductivity results from gas adsorption which can provide efficient electrical responses via gas adsorption. The blue/red shift in the optical response proved to be a way of detecting the types of adsorbed gases. The adsorption of O3 is exothermic and spontaneous whereas the adsorption of SO2 is endothermic and non-spontaneous. The negative change in entropy verifies the thermodynamic stability of all the complexes. QTAIM analysis reveals strong covalent or partial covalent interactions between absorbent and adsorbate. The significant variation in electrical and optical response with optimal adsorbent-gas interaction strength makes both TGC and PTGC promising candidates for O3 and SO2 sensing.

Understanding the mechanism for initial deposition under the coupling effect of sodium and calcium during boiler operation: The first-principles study and thermodynamic analysis

During the boiler operation, ash deposition can result in a decrease in boiler efficiency and an enhanced release of pollutants. To relieve these issues, the formation mechanism for initial deposition triggered by the coupling effect of sodium and calcium was investigated by the first-principles study in this paper. The results indicated that the binding of sodium and calcium deposited on Fe3O4(001) surface is non-covalent interaction. Furthermore, |V|/G values of different particles on the surface are less than 2 and closed to 1. So the reactions of sodium and calcium deposited on the Fe3O4(001) are mainly closed-shell interactions accompanied by partial covalent interaction by Atom-in-Molecule theory. Additionally, the position and form of weak interaction also be further clarified by the independent gradient model. The thermodynamic calculation results showed that Gibbs free energy change is more affected to the change of the temperature under the existence of sodium and calcium. The reaction equilibrium constants is larger than 1, indicating that sodium and calcium are easily combined with Fe3O4(001). Moreover, calcium is more likely to promote a positive reaction than sodium.

DFT-based modeling of polypyrole/B12N12 nanocomposite for the photocatalytic applications

Boron-based nanocomposites considered as one of the most promising photocatalysts, have drawn significant attention in the degradation of pollutants in aquatic environments. In this regard, density functional theory calculations were carried out on the B12N12 nanocluster interacted with various lengths of (PPy)n oligomers (n = 3, 5, 7, and 9) to predict the optical, electronic, charge transfer properties as well as the optimum composition of obtained (PPy)n/B12N12 nanocomposites. It was found that the most stable nanocomposite corresponds to (PPy)3/B12N12, which was supported by its greatest adsorption energy (−59.460 kcal mol−1) in the gas phase. The calculations in the gas phase and water showed that water as a solvent has a key role in the interaction between B12N12 nanocluster and (PPy)n oligomers. The results revealed that the adsorption of (PPy)9 oligomer on the B12N12 nanocluster leads to the highest reduction (∼ 2.672 eV) in the energy gap (Eg) value, while the lowest reduction (∼ 1.475 eV) was related to (PPy)3/B12N12 nanocomposite. Moreover, the natural bond orbital analysis showed that the charge flows from (PPy)n oligomers to the B12N12 nanocluster. Polarizability (α0) and first hyperpolarizability (β0) values revealed that the adsorption of (PPy)9 oligomer on the surface of B12N12 nanocluster has the most considerable effect on the optical response of B12N12 nanocluster due to increasing the α0 and β0 values about 492.49 and 5070.07 a.u, respectively. The UV–Vis spectra analysis showed that the (PPy)9/B12N12 nanocomposite has the highest bathochromic shift (∼ 245.39 nm) among other nanocomposites. Finally, quantum theory of atoms in molecules analysis showed that (PPy)n oligomers interact with B12N12 nanocluster through the partial covalent interactions.

Spectroscopic investigation of the covalence of An(III) complexes with tetraethylcarboxamidopyridine.

In this work, we report a combined NMR spectroscopic and time-resolved laser fluorescence spectroscopic (TRLFS) study of the complexation of N,N,N',N'-tetraethyl-2,6-carboxamidopyridine (Et-Pic) with Ln(III) (La, Sm, Eu, and Lu), Y(III) and An(III) (Am and Cm). The focal point of this study was the metal-ligand interaction in the [M(Et-Pic)3]3+ (M = An and Ln) complexes. The NMR analyses found slight differences between the An(III)-N and Ln(III)-N interactions in contrast to the similar properties of the Am(III)-O and Ln(III)-O interactions. These results were supported by TRLFS which shows that the 1 : 3 Cm(III) complex is by one order of magnitude more stable than the respective Eu(III) complex. Thus, the ligand's selectivity lies in between those of pure N- and O-donor ligands. The selectivity results from a small partial covalent bonding between the An(III) ions and Et-Pic.

Effect of mono-vacant defects on the adsorption properties of deep eutectic solvents onto hexagonal boron-nitride nanoflakes

Hexagonal boron nitride is a promising material for a variety of electronic, optical, and material science applications. Both the synthesis of the material through exfoliation, and its various applications almost inevitably require its solvation. Deep eutectic solvents (DES) are extremely useful solvents for these types of applications due to their non-volatility, inflammability, biocompatibility, and reasonable cost. There are many different deep eutectic solvents available, and their suitability for any given application is particularly dependent on the specific of their structure. DES have been examined computationally for use with boron nitride, but these calculations use idealized, perfect boron nitride sheets instead of the more realistic, defect-containing systems. In this report, we investigated four DESs with two experimentally observed defective boron nitride, one with a single boron vacancy, the other with a single nitrogen vacancy. All DESs bound with higher affinity to the defective boron nitride than to the pristine surface. Charge transfer was minimal in all cases although the surfaces tended to donate electron density to the solvents. The interactions between the solvents and the surfaces are primarily non-covalent although in several cases natural bond order analysis indicates a partial covalent interaction that helps explain the higher-than-expected affinity for particular DES. The DESs have little effect on the predicted optical behaviour of the pristine boron nitride but do significantly change the adsorption spectrum of the defective boron nitride nanoflakes; the effect on bulk material might be limited. Together these results suggest that the choice of DES can either be made to limit any effect on the properties of the material (urea-choline chloride) or to affect the optical and electronic nature of the material (benzoic acid-choline chloride).

Effect of substitution on the bonding in He dimer confined within dodecahedrane: A computational study.

The effect of substitution in the dodecahedrane (C20 H20 ) cage on bonding in the confined He dimer is analyzed. The HeHe distances inside the halogenated dodecahedrane C20 X20 (X = FBr) cages are found to be less than half of that in the free He dimer. Comparing the equilibrium structure of He2 @C20 H20 with He2 @C20 X20 at ωB97XD/def2-TZVPP level, it is found that the He-He distances are relatively larger in the latter cases indicating the influence of halogen groups on the interaction between the cage and the trapped He pair. The viability of the He2 @C20 X20 complexes is reflected in the presence of a very high activation energy barrier against the thermochemically feasible dissociation process producing free He2 and C20 X20 . Quantum theory of atoms in molecules (QTAIM) approach reveals a partial covalent interaction between He pair.

Understanding the mechanism of H2S oxidation by flavin-dependent sulfide oxidases: a DFT/IEF-PCM study.

In the last years, H2S has been recognized as a signaling molecule in mammals, which can synthesize and catabolize (by oxidation) such species. The latter process is accelerated by a sulfide:quinone oxidoreductase (SQR, E.C. 1.8.5.4), a flavin-dependent sulfide oxidase (FDSO). FDSOs catalyze electron transfer from H2S to an acceptor in catalytic cycles involving two phases: (I) reduction of FAD by H2S (SH-) and (II) electron transfer from FADH- to the electron acceptor. The first step of FAD reduction consists on the reaction of SH- with a catalytic disulfide at the active site of the enzyme, to yield a thiolate and a persulfide in the protein. This step is ca. 106 times faster than the analogous reaction with low-molecular-weight disulfides (LMWDs) and the causes of such extraordinary acceleration remain unknown. Using the IEF-PCM(ε ≈ 10)/M06-2X-D3/6-31+G(d,p) level of theory, we have modeled the reaction of SH- with a disulfide as located in a representative model of the active site extracted from a prokaryotic SQR, assessing the effects of partial covalent interactions (PCIs) between the leaving sulfur atom and flavin ring on the activation Gibbs free-energy barrier at 298K (∆‡G298K). To also evaluate the importance of entropic penalties on the first step, we have modeled at the same level of theory the reaction of (bis)hydroxyethyl disulfide in aqueous solution, a LMWD for which experimental data is available. Our results show that PCIs between the leaving sulfur atom and the flavin group only have a minor effect (∆‡G298Kreduced by 1.6kcalmol-1) while compensating entropic penalties could have a much larger effect (up to 8.3kcalmol-1). Finally, we also present here a first model of some of further steps in the phase I of the catalytic cycle as in mammalian FDSOs, providing some light about their detailed mechanism. Graphical abstract .

Coordination numbers in hydrated Cu(II) ions.

The potential energy surface of [Cu(H2O)n]2+ clusters with n = 12, 16, and 18 was explored by using a modified version of the simulated annealing method. Such exploration was carried out by using the PM7 semiempirical method to obtain around 100,000 isomers, which provide candidates to be optimized with PBE0-D3, M06-2X, and BHLYP exchange-correlation functionals coupled with the 6-311++G** basis set. These methods based on the Kohn-Sham approach delivered isomers with coordination numbers of 4, 5, and 6. The analysis used to obtain coordination numbers was based on geometrical parameters and the quantum theory of atoms in molecules (QTAIM) approach. Our methodology found only one isomer with fourfold coordination and its probabilities to appear in these clusters are quite small for high temperatures. The procedure used in this article predicts important populations of fivefold and sixfold coordination clusters, in fact, the fivefold coordination dominates for PBE0-D3 and BHLYP methods, although the sixfold coordination starts to be important when the number of water molecules is increased. The nature of axial and equatorial contacts is discussed in the context of the QTAIM and the noncovalent interaction index (NCI), which gives a clear classification of such orientations. Also, these methods suggest a partial covalent interaction between the Cu2+ and water molecules in both positions; equatorial and axial.

Holistic Approach to Partial Covalent Interactions in Protein Structure Prediction and Design with Rosetta

Partial covalent interactions (PCIs) in proteins, which include hydrogen bonds, salt bridges, cation-π, and π-π interactions, contribute to thermodynamic stability and facilitate interactions with other biomolecules. Several score functions have been developed within the Rosetta protein modeling framework that identify and evaluate these PCIs through analyzing the geometry between participating atoms. However, we hypothesize that PCIs can be unified through a simplified electron orbital representation. To test this hypothesis, we have introduced orbital based chemical descriptors for PCIs into Rosetta, called the PCI score function. Optimal geometries for the PCIs are derived from a statistical analysis of high-quality protein structures obtained from the Protein Data Bank (PDB), and the relative orientation of electron deficient hydrogen atoms and electron-rich lone pair or π orbitals are evaluated. We demonstrate that nativelike geometries of hydrogen bonds, salt bridges, cation-π, and π-π interactions are recapitulated during minimization of protein conformation. The packing density of tested protein structures increased from the standard score function from 0.62 to 0.64, closer to the native value of 0.70. Overall, rotamer recovery improved when using the PCI score function (75%) as compared to the standard Rosetta score function (74%). The PCI score function represents an improvement over the standard Rosetta score function for protein model scoring; in addition, it provides a platform for future directions in the analysis of small molecule to protein interactions, which depend on partial covalent interactions.

Iron sandwiched between group 13 analogues of N-Heterocyclic carbene: A theoretical investigation

The present article discusses a theoretical possibility of a novel class of sandwiched organometallic compounds based on the group 13 analogues of N-Heterocyclic carbene. The structure, stability and bonding pattern of the Fe(NHE)2 complexes (where E = B, Al and Ga) have been studied using density functional theory. The bond dissociation energy and binding energy are comparable with ferrocene. In addition, the topological study of the electron density describes the partial covalent interaction of the ligands with the metal atom. The synthetic possibility of such complexes with bulky substituent at the nitrogen center are addressed as well.

Clˉ as the halogen bond acceptor: studies on strong halogen bonds

The Clˉ anion as the halogen bond acceptor, the diiodotetrafluoroethane I(CF2)2I and its derivatives I(MF2)nI (M = C, Si, Ge, Sn) as the halogen bond donor, and the strong halogen bonds could be formed. The halogen bonds between I(MF2)nI and Clˉ have been designed and investigated by Moller–Plesset perturbation/aug-cc-pVDZ calculations together with the aug-cc-pVDZ-pp basis set for iodine and stannum. The halogen bonds in the I(MF2)nI∙∙∙Clˉ complexes are strong, which are apparently related to the group IV elements, becoming stronger along the sequence of M = Si, C, Ge, Sn. Accompanied with increasing number (n) of MF2 unit, the halogen bonds (M = Si, Ge, Sn) also become stronger. The energy decomposition analyses reveal that the exchange energy contributes most in forming these halogen-bonded interactions. In the meantime, the electrostatic energy is also a significant factor for the I∙∙∙Clˉ interactions. The halogen bonds of I(MF2)nI∙∙∙Clˉ(M = C, Ge, Sn) belong to partial-covalent interactions, while they are noncovalent interactions when M = Si.

Comparative studies on group III σ-hole and π-hole interactions.

The σ-hole of M2 H6 (M = Al, Ga, In) and π-hole of MH3 (M = Al, Ga, In) were discovered and analyzed, the bimolecular complexes M2 H6 ···NH3 and MH3 ···N2 P2 F4 (M = Al, Ga, In) were constructed to carry out comparative studies on the group III σ-hole interactions and π-hole interactions. The two types of interactions are all partial-covalent interactions; the π-hole interactions are stronger than σ-hole interactions. The electrostatic energy is the largest contribution for forming the σ-hole and π-hole interaction, the polarization energy is also an important factor to form the M···N interaction. The electrostatic energy contributions to the interaction energy of the σ-hole interactions are somewhat greater than those of the π-hole interactions. However, the polarization contributions for the π-hole interactions are somewhat greater than those for the σ-hole interactions.

Computational design of protein-small molecule interfaces

The computational design of proteins that bind small molecule ligands is one of the unsolved challenges in protein engineering. It is complicated by the relatively small size of the ligand which limits the number of intermolecular interactions. Furthermore, near-perfect geometries between interacting partners are required to achieve high binding affinities. For apolar, rigid small molecules the interactions are dominated by short-range van der Waals forces. As the number of polar groups in the ligand increases, hydrogen bonds, salt bridges, cation-π, and π-π interactions gain importance. These partial covalent interactions are longer ranged, and additionally, their strength depends on the environment (e.g. solvent exposure). To assess the current state of protein-small molecule interface design, we benchmark the popular computer algorithm Rosetta on a diverse set of 43 protein-ligand complexes. On average, we achieve sequence recoveries in the binding site of 59% when the ligand is allowed limited reorientation, and 48% when the ligand is allowed full reorientation. When simulating the redesign of a protein binding site, sequence recovery among residues that contribute most to binding was 52% when slight ligand reorientation was allowed, and 27% when full ligand reorientation was allowed. As expected, sequence recovery correlates with ligand displacement.

Probing the Chemical Bonding and Electron Structure of the Benzoate model for Fe-MoF-5

ABSTRACTUsing first-principles density functional theory, we investigated the chemical bonding and electronic structure of the metal-organic-framework with individual structural element OFe4(CO2Ph)6. The calculations showed that there is no obvious structural difference between OFe4(CO2Ph)6 and OZn4(CO2Ph)6. The analysis of electronic structure and chemical bonding reveals that the Fe-O has mainly ionic interaction and partial covalent interaction while O-C, H-C and C-C exhibit mainly covalent interactions. The finding in this paper may shed light on the synthesis of MOF-5 materials with other metal centers.

Synthesis of a Uranyl Persulfide Complex and Quantum Chemical Studies of Formation and Topologies of Hypothetical Uranyl Persulfide Cage Clusters

The compound Na(4)[(UO(2))(S(2))(3)](CH(3)OH)(8) was synthesized at room temperature in an oxygen-free environment. It contains a rare example of the [(UO(2))(S(2))(3)](4-) complex in which a uranyl ion is coordinated by three bidentate persulfide groups. We examined the possible linkage of these units to form nanoscale cage clusters analogous to those formed from uranyl peroxide polyhedra. Quantum chemical calculations at the density functional and multiconfigurational wave function levels show that the uranyl-persulfide-uranyl, U-(S(2))-U, dihedral angles of model clusters are bent due to partial covalent interactions. We propose that this bent interaction will favor assembly of uranyl ions through persulfide bridges into curved structures, potentially similar to the family of nanoscale cage clusters built from uranyl peroxide polyhedra. However, the U-(S(2))-U dihedral angles predicted for several model structures may be too tight for them to self-assemble into cage clusters with fullerene topologies in the absence of other uranyl-ion bridges that adopt a flatter configuration. Assembly of species such as [(UO(2))(S(2))(SH)(4)](4-) or [(UO(2))(S(2))(C(2)O(4))(4)](4-) into fullerene topologies with ~60 vertices may be favored by use of large counterions.

Thermodynamics for the clustering of ammonia onto lead(1+) in the gas-phase

Equilibrium constants together with the enthalpy, entropy, and Gibbs free energy changes were determined for the gas-phase stepwise addition reactions of up to four ammonia molecules onto the Pb{sup +} ion. Standard enthalpy changes of -28.3, -19.2, -13.0, and -10.7 kcal/mol and entropy changes of -23.3, -27.3, -22.0, and -24.8 cal/K {center dot} mol were measured for the first, second, third, and fourth steps of the clustering, respectively. These results, along with earlier ones for the clustering of ammonia onto Li{sup +}, Na{sup +}, K{sup +}, and Rb{sup +}, provide evidence concerning the structure and types of bonding in metal ion-ammonia clusters. Since the binding in Pb{sup +}NH{sub 3} and Pb{sup +}(NH{sub 3}){sub 2} is much stronger than that expected by electrostatic calculation, partial covalent interaction of Pb{sup +} with NH{sub 3} is likely in these two clusters. Theoretical calculations were also carried out with the Sakur-Tetrode equation to determine the contributions of the translational, rotational, and vibrational components to the entropy change for each of the above clustering reactions.