Natural Bond Orbital Methodologies Research Articles

Theoretical investigations into the bonding and separation properties of non-rigid, partially rigid, and rigid ligands derived from Et-Tol-PTA with trivalent lanthanides and actinides.

The separation of trivalent actinide elements from lanthanide elements represents one of the most formidable challenges within the context of nuclear waste partitioning and transmutation (P&T) processes. Consequently, we embarked on a systematic investigation aimed at elucidating the bonding properties and thermodynamic behavior of a N-ethyl-N-tolyl-2-amide-1,10-phenanthroline (Et-Tol-PTA) ligand in conjunction with trivalent actinide and lanthanide elements. This investigation involved the utilization of various density functional theory (DFT) methods and a comparative analysis between small-core pseudopotential basis sets and all-electron basis sets. It was found that well-performing results were achieved using the PBE0 functional in both bond length and thermodynamic energy calculations, with minimal impact being exerted by the basis set on the results. Furthermore, an exploration was carried out into the bonding and thermodynamic properties of trivalent actinides and lanthanides with ligands derived from Et-Tol-PTA, encompassing non-rigid (La), partially rigid (Lb, Lc), and rigid (Ld) ligands. Thermodynamically, advantages in the separation of Am(III)/Eu(III) were exhibited by Lb and Lc ligands, while excellent performance in the separation of Am(III)/Cm(III) was demonstrated by the La ligand. Analyses conducted using quantum theory of atoms in molecules (QTAIM), reduced density gradient (RDG), and natural bond orbital (NBO) methodologies revealed the presence of partial covalent character in the bonds between oxygen (O) and metal (M), as well as between nitrogen (N) and metal (M), with a higher degree of covalent character being observed in O-Am and N-Am bonds compared to O-Cm/Eu and N-Cm/Eu interactions.

Assessing the efficacy of aluminum metal clusters Al13 and Al15 in mitigating NO2 and SO2 pollutants: a DFT investigation.

The present investigation delves into the adverse environmental impact of atmospheric pollutant gases, specifically nitrogen dioxide (NO2) and sulfur dioxide (SO2), which necessitates the identification and implementation of effective control measures. The central objective of this study is to explore the eradication of these pollutants through the utilization of aluminum Al13 and Al15 metal clusters, distinguished by their unique properties. The comprehensive evaluation of gas/cluster interactions is undertaken employing density functional theory (DFT). Geometric optimization calculations for all structures are executed using the ωB97XD functional and the Def2-svp basis set. To probe various interaction modalities, gas molecule distribution around the metal clusters is sampled using the bee colony algorithm. Frequency calculations employing identical model chemistry validate the precision of the optimization calculations. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) methodologies are applied for the analysis of intermolecular interactions. This research establishes the robust formation of van der Waals attractions between the investigated gas molecules, affirming aluminum metal clusters as viable candidates for the removal and control of these gases.

Hydrogen Bonding, π-Stacking, and Aurophilic Interactions in Two Dicyanoaurate(I)-based Manganese(II) Complexes with Auxiliary Bis-Pyridine Ligands.

The relevance of hydrogen-bonding, π-π stacking and aurophilic interactions in the solid-state of two new heterobimetallic (AuI-MnII) complexes is analyzed in this manuscript. They are discrete complexes of formulae [Mn(bipy)2(H2O){Au(CN)2}][Au(CN)2] and [Mn(dmbipy)2{Au(CN)2}]·H2O, (bipy = 2,2'-bipyridine and dmbipy = 5,5'-dimethyl-2,2'-bipyridine), which are based on dicyanidoaurate(I) groups and 2,2'-bipyridyl-like co-ligands. They have been synthesized in good yields and X-ray characterized. In both compounds, aurophilic, OH···N hydrogen bonding and π-π interactions governed the supramolecular assemblies in the solid state. These contacts with special emphasis on the aurophilic interactions have been studied using density functional theory calculations and characterized using the quantum theory of atoms-in-molecules and the noncovalent interaction plot. The aurophilic contacts have been also rationalized from an orbital point of view using the natural bond orbital methodology, evidencing stabilization energies up to 5.7 kcal/mol. Moreover, the interaction energies have been decomposed using the Kitaura-Morokuma energy decomposition analysis, confirming the importance of electrostatic and orbital effects.

The synergistic co-operation of N-H...O=P hydrogen bonds and C-H...OX weak intermolecular interactions (X is =P or -C) in the (CH3O)2P(O)(NH-NHC6F5) amidophosphoester: a combined X-ray crystallographic and theoretical study.

The asymmetric unit of O,O'-dimethyl [(2,3,4,5,6-pentafluorophenyl)hydrazinyl]phosphonate, C8H8F5N2O3P, is composed of two symmetry-independent molecules with significant differences in the orientations of the C6F5 and OMe groups. In the crystal structure, a one-dimensional assembly is mediated from classical N-H...O hydrogen bonds, which includes R22(8), D(2) and some higher-order graph-set motifs. By also considering weak C-H...O=P and C-H...O-C intermolecular interactions, a two-dimensional network extends along the ab plane. The strengths of the hydrogen bonds were evaluated using quantum chemical calculations with the GAUSSIAN09 software package at the B3LYP/6-311G(d,p) level of theory. The LP(O) to σ*(NH) and σ*(CH) charge-transfer interactions were examined according to second-order perturbation theory in natural bond orbital (NBO) methodology. The hydrogen-bonded clusters of molecules, including N-H...O and C-H...O interactions, were constructed as input files for the calculations and the strengths of the hydrogen bonds are as follows: N-H...O [R22(8)] > N-H...O [D(2)] > C-H...O. The decomposed fingerprint plots show that the contribution portions of the F...H/H...F contacts in both molecules are the largest.

Intermolecular complexes of halocyclopropenone derivatives with the hypohalousacids HOF, HOCl, HOBr, and HOI

The intermolecular interactions between halocyclopropenone derivatives (HC$_{3}$OX; X $=$ I, Br, Cl, and F) and hypohalous acids (HOY; Y $=$ I, Br, Cl, and F) were studied via the MP2 method utilizing the aug-cc-pVTZ and aug-cc-pVTZ(-PP) basis sets. The three types of complexes were hydrogen bonds, halogen bonds, and complexes containing both hydrogen and halogen bonds. The results obtained indicated that interactions in the Type 1 complexes were stronger than those in Types 2 and 3. The H-O bonds revealed red shifts with complex formation in Types 1 and 2. The O-Y bonds displayed red shifts in the Type 3 and blue shifts in the Type 2 structures. Molecular electrostatic potential, quantum theory of atoms in molecules, and natural bond orbital methodologies were used to analyze these interactions.

Interactions of sodium polystyrene sulfonate with 4-methylpyridinium based ionic liquids in aqueous solution: Viscometry, conductometry, UV–Vis spectroscopy and density functional theory studies

Viscosity (η) and molar conductivity (Λ) of aqueous solutions of sodium polystyrene sulfonate (NaPSS) in the presence of some 4-methylpyridinium based ionic liquids (1-Butyl-4-methylpyridinium bromide [BMPyr]Br, 1-Hexyl-4-methylpyridinium bromide [HMPyr]Br and 1-Octyl-4-methylpyridinium bromide [OMPyr]Br) were investigated at T = (288.15, 298.15 and 308.15) K. The viscosity values were correlated with the Wolf equation to obtain the intrinsic viscosity ([η]) of NaPSS. The intrinsic viscosity of NaPSS decreases by increasing the concentration of ionic liquids due to screens effects of ionic liquids and decreased with increasing alkyl chain length of ILs. The scaling theory is used for the description of electrical conductance of polyelectrolytes. The values of fractions of uncondensed counterions f have been estimated. The effects of the polyelectrolyte concentration, the relative permittivity of the medium, different alkyl chain length and the temperature on the fractions of uncondensed counterions of NaPSS aqueous solutions have been discussed. UV–Vis spectroscopy and Quantum chemical calculations studies are also used to confirm the existence of interactions between NaPSS and ILs. The UV–Vis spectra of NaPSS show that the conformation of NaPSS changes in the presence of ionic liquids; therefore the value of electric multipole moment decreases. Consequently, the absorption intensity of NaPSS was decreased with the addition of ionic liquids. Density functional theory (DFT) has been used to investigate the interactions between [PSS]− anion and [RMPyr]+ cations. The molecular electrostatic potential, natural bond orbital methodologies and atoms in molecules are used to analyses the nature of interactions of the ion-pairs [RMPyr]+[PSS]−.

A combined X-ray crystallography and theoretical study of N-H...OX (X is =P and -C) hydrogen bonds in two new structures with a (C-O)2(N)P(=Y) (Y is O and S) skeleton.

The crystal structures of N,N'-(cyclohexane-1,4-diyl)bis(O,O'-diphenylphosphoramide), C30H32N2O6P2 or (C6H5O)2P(O)(1-NH)(C6H10)(4-NH)P(O)(OC6H5)2, (I), and N,N'-(1,4-phenylene)bis(O,O'-dimethylthiophosphoramide), C10H18N2O4P2S2 or (CH3O)2P(S)(1-NH)(C6H4)(4-NH)P(S)(OCH3)2, (II), have been investigated. In the structure of (I), with an (O)2(N)P(O) skeleton, two symmetry-independent phosphoramide molecules are linked through N-H...O=P hydrogen bonds. In the structure of (II), with an (O)2(N)P(S) skeleton, the ester O atoms take part in N-H...O-C hydrogen bonds as acceptors; the P=S groups do not participate in hydrogen-bonding interactions. The strengths of these hydrogen bonds were evaluated, using quantum chemical calculations with the GAUSSIAN09 software package at the B3LYP/6-311G(d,p) level of theory. For this, LP(O) to σ*(NH) charge transfers were studied, according to the second-order perturbation theory in natural bond orbital (NBO) methodology, for a three-component cluster of hydrogen-bonded molecules for both structures, including all of the independent N-H...O hydrogen bonds observed in the crystal packing. The details of the intermolecular interactions were studied by Hirshfeld surface maps and two-dimensional fingerprint plots.

Evaluation of N-H...S and N-H...π interactions in O,O'-diethyl N-(2,4,6-trimethylphenyl)thiophosphate: a combination of X-ray crystallographic and theoretical studies.

In the crystal structure of O,O'-diethyl N-(2,4,6-trimethylphenyl)thiophosphate, C13H22NO2PS, two symmetrically independent thiophosphoramide molecules are linked through N-H...S and N-H...π hydrogen bonds to form a noncentrosymmetric dimer, with Z' = 2. The strengths of the hydrogen bonds were evaluated using density functional theory (DFT) at the M06-2X level within the 6-311++G(d,p) basis set, and by considering the quantum theory of atoms in molecules (QTAIM). It was found that the N-H...S hydrogen bond is slightly stronger than the N-H...π hydrogen bond. This is reflected in differences between the calculated N-H stretching frequencies of the isolated molecules and the frequencies of the same N-H units involved in the different hydrogen bonds of the hydrogen-bonded dimer. For these hydrogen bonds, the corresponding charge transfers, i.e. lp (or π)→σ*, were studied, according to the second-order perturbation theory in natural bond orbital (NBO) methodology. Hirshfeld surface analysis was applied for a detailed investigation of all the contacts participating in the crystal packing.

The triel bond: a potential force for tuning anion–π interactions

ABSTRACTUsing ab-initio calculations, the mutual influence between anion–π and B···N or B···C triel bond interactions is investigated in some model complexes. The properties of these complexes are studied by molecular electrostatic potential, noncovalent interaction index, quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses. According to the results, the formation of B···N or B···C triel bond interactions in the multi-component systems makes a significant shortening of anion–π distance. Such remarkable variation in the anion–π distances has not been reported previously. The strengthening of the anion–π bonding in the multi-component systems depend significantly on the nature of the anion, and it becomes larger in the order Br− > Cl− > F−. The parameters derived from the QTAIM and NBO methodologies are used to study the mechanism of the cooperativity between the anion–π and triel bond interactions in the multi-component complexes.

Unimolecular rearrangement of the simplest compound models with a selenium–oxygen, selenium–sulphur and selenium–selenium bond: SeXH and HSeXH (X = O,S,Se)

ABSTRACTThe aim of this study was to characterise the simplest compound models with a selenium–oxygen, selenium–sulphur and selenium–selenium bond as the SeXH and HSeXH isomers (X = O,S,Se). One of the main aspects of this investigation was to provide a description on the isomerisation pathways involving 2[H,Se,X] and 1[2H,Se,X] potential energy surfaces calculated at the CCSD(T)/CBS//MP2/cc-pVTZ level. The energy difference was 13 kcal mol−1 between hydroxyselenide (SeOH) and oxoselenium (HSeO), while a gap of 3 kcal mol−1 was predicted between thiol-selenide (SeSH) and selenol-sulphide (HSeS). The SeOH→HSeO unimolecular rearrangement showed a barrier energy of 44.6 kcal mol−1, decreasing almost two times in sulphur and selenium analogous reactions. In addition, hydroxyselenide (HSeOH), thioselenenic acid (HSeSH) and diselane (HSeSeH) were the global minimum configurations in the ground state, while the energy differences among the other isomers were close to 30 kcal mol−1. The HSeXH→H2SeX and HSeXH→SeXH2 isomerisations showed barrier energies ranging from 40 to 65 kcal mol−1, while these reverse routes presented heights that were three times smaller. The kinetic rate constant of each 1,2-H shift reaction was performed here as well as an analysis of the selenium-chalcogen bonds using natural bond orbital and bond order index methodologies.

The enhancing effect of a cation-π interaction on the cooperativity of halogen bonds: A computational study

In this work, we investigate the effect of a cation-π interaction on the cooperativity of X⋯N halogen bonds in PhX⋯NCX⋯NH3 complexes, where Ph=phenyl and X=Cl, Br, I. Molecular geometries and interaction energies of the resulting complexes are studied at the MP2/aug-cc-pVDZ(-PP) computational level. The mechanism of the cooperativity between halogen bonds is analyzed using parameters derived from the noncovalent index, quantum theory of atoms in molecules and natural bond orbital methodologies. It is found that the divalent cations (Be2+, Mg2+) have a larger influence on the cooperativity of halogen bonds than monovalent ones (Li+, Na+). The formation of a cation-π interaction leads to strengthening of the halogen bonds, hence increases their cooperativity.

A new approach on diminutive effects for non-covalent interactions: fused bicyclic hydrogen-bonded complexes of hypohalous acids with fluoromethanol

ABSTRACTThe computational study of dimer and trimer complexes of fluoromethanol (CH2FOH) with one or two molecules of hypohalous acids (HOX; X = F, Cl or Br) was carried out at the MP2/aug-cc-pVDZ computational level. Also to show the reliability of these results, the binding distance and interaction energy have been compared with large basis set aug-cc-pVTZ level for some systems. The 1:1 ratio gives two different hexagonal and heptagonal ring complexes and the 1:2 ratio of CH2FOH/HOX leads to fused bicyclic hydrogen-bonded trimer adducts constructed from hexagonal and heptagonal rings. The results show diminutive effects in the range of 0.36–0.78 kcal/mol for the trimer bicyclic systems. Redshifts with bond elongations were observed for H–O and C–F bonds, while blueshifts along with bond contractions were seen for the C–H and the X–O bonds. The CH2FOH/HOX complexes were analysed using the Quantum Theory of Atoms in Molecules (QTAIM) and natural bond orbital methodologies.

Computational study of the cooperative effects between tetrel bond and halogen bond in XCN⋅⋅⋅F2CO⋅⋅⋅YCN complexes (X = H, F, Cl, Br; Y = F, Cl, Br)

ABSTRACTAb initio calculations have been accomplished to study the cooperativity between the halogen bond and tetrel bond in the XCN⋅⋅⋅F2CO⋅⋅⋅YCN (X = H, F, Cl, Br; Y = F, Cl, Br) complexes. F2CO at the same time plays the role of Lewis acid with the π-hole on the C atom and Lewis base with the O atom to participate in the tetrel bond and in halogen bond, respectively. According to the geometry survey, the effect of a tetrel bond on a halogen bond is more pronounced than that of a halogen bond on a tetrel bond and the intermolecular distances in the triads are always smaller than the corresponding values in the dyads. In all cases, the halogen bond and tetrel bond in the termolecular complexes are stronger compared with those in the bimolecular complexes. So, from the intermolecular distances, interaction energies and many-body interactions demonstrate that there is positive cooperativity between the halogen bond and tetrel bond. The molecular electrostatic potential, atoms in molecules and natural bond orbital methodologies are used to analyse the nature of interactions of the complexes.

Theoretical insight into the interplay between lithium and halogen–hydride bonds: Anab initiostudy

Quantum chemical calculations have been performed to analyze the intermolecular interactions in the ternary NCLi ⋯ NCX ⋯ HMgY complexes ( X = F , Cl , Br ; Y = H , F , Cl , Br , Li ). A cooperative effect is observed between the lithium and halogen–hydride bonds in these complexes. The cooperative energy ranges from -1.81 kJ/mol to -5.21 kJ/mol, -3.59 kJ/mol to -9.86 kJ/mol and -4.77 kJ/mol to -14.27 kJ/mol for X = F , Cl and Br , respectively (at MP2/6-311++G(d,p) level). The geometrical and interaction energies analysis reveal that the lithium bond has a greater enhancing effect on the halogen–hydride bond. The results of many-body analysis indicate that two- and three-body interaction energies have a positive contribution to the total interaction energy. The electronic characteristics of the complexes have been analyzed through molecular electrostatic potential (MEP), atoms in molecules (AIM), electron localization function (ELF) and natural bond orbital (NBO) methodologies.

Theoretical study of intermolecular interactions in CB4H8–HOX (X = F, Cl, Br, I) complexes

The molecular aggregation based on intermolecular interactions between CB4H8 and HOX (X=F, Cl, Br and I) with particular emphasis on their bonding characteristics have been investigated using second order Moller–Plesset perturbation (MP2) method with aug-cc-pVDZ basis set. Different kinds of interactions including hydrogen bond (HB; H⋯O, XH; H⋯X), dihydrogen bond (DiHB; H⋯H) and non-classical B–B⋯H interactions were found between CB4H8 and HOX molecules. The structures of complexes have been analyzed using AIM and natural bond orbital methodologies. Good correlations have been found between the interaction energies (SE), the second-order perturbation energies E(2), and the charge transfer qCT in the studied systems.

Aromatic Amino Acids-Guanidinium Complexes through Cation-π Interactions.

Continuing with our interest in the guanidinium group and the different interactions than can establish, we have carried out a theoretical study of the complexes formed by this cation and the aromatic amino acids (phenylalanine, histidine, tryptophan and tyrosine) using DFT methods and PCM-water solvation. Both hydrogen bonds and cation-π interactions have been found upon complexation. These interactions have been characterized by means of the analysis of the molecular electron density using the Atoms-in-Molecules approach as well as the orbital interactions using the Natural Bond Orbital methodology. Finally, the effect that the cation-π and hydrogen bond interactions exert on the aromaticity of the corresponding amino acids has been evaluated by calculating the theoretical NICS values, finding that the aromatic character was not heavily modified upon complexation.

Theoretical Investigation of Proton Transfer in Thiazolidine-2-thione and Oxazolidine-2-thione via Direct Transition and Self-Assisted and Water-Assisted Tautomerization

Thione–thiol transformation of thiazolidine-2-thione and oxazolidine-2-thione via direct transition, as well as self-assisted and water-assisted tautomerization was investigated using the quantum-chemical calculations. The thione complexes are more stable than the corresponding thiols. The calculations revealed that the proton transfer energy barriers are significantly lower in the presence of water molecules. Direct transition is more difficult than the water-assisted and self-assisted processes. The cooperative effects in terms of additive interaction energies and cooperativity factors of the clusters are measured and discussed. The electronic properties of the complexes are analyzed using parameters derived from atoms-in-molecules and natural bond orbital methodologies. Also, the influence of the hydrogen bond on the molecular and topological properties, as well as nuclear magnetic resonance one- and two-bond spin–spin coupling constants are investigated.

Substituent effects in cooperativity of chalcogen bonds

In the present work, substituent effects on cooperativity of S···N chalcogen bonds are studied in XHS···NCHS···4-Z–Py (X = F, Cl; Z = H, F, OH, CH3, NH2, NO2, and CN; and Py = pyridine) complexes using ab initio calculations. An increased attraction or a positive cooperativity is observed on introduction of a third molecule to the XHS···NCHS and NCHS···4-Z–Py binary systems. The shortening of each chalcogen bond distance in the ternary systems is dependent on the substituent Z and is increased in the order Z = NH2 > OH > CH3 > H > F > CN > NO2. The electronic aspects of the complexes are analysed using molecular electrostatic potential, and the parameters derived from the atoms in molecules and natural bond orbital methodologies. According to interaction energy decomposition analysis, the electrostatic energies are important in the interaction energy of S···N bonds and may be regarded as being responsible for the stability of these complexes.

Synthesis, Structures, and DFT Study of CuBr Based Coordination Polymers via in Situ Reduction of Copper(II)

This paper describes the one-pot synthesis of two CuBr based coordination polymers, {[Cu(μ2-L1)Br]·1.87H2O}n (1) and {[Cu(μ2-L2)Br]·C4H10O}n (2), where L1 = 2,3-dihydro-5,6-bis(4-methoxyphenyl)pyrazine and L2= 5,6-diphenyl-2,3-dihydropyrazine, upon reduction of copper(II) at ambient conditions. The structures have been confirmed by single crystal X-ray diffraction analysis. Both complexes are found to be highly inert toward oxidation. Finally, a density functional theory (DFT) study of the energetic features of several noncovalent interactions observed in the solid state has been analyzed and characterized using Bader’s theory of “atoms in molecules” and the cuprophilic interactions in complex 2 using natural bond orbital methodology.

Chiral discrimination in dimers of diphosphines PH₂-PH₂ and PH₂-PHF.

A theoretical study of the conformational profile of two diphosphines, PH2-PH2 and PH2-PHF, is carried using second-order Møller-Plesset perturbation theory (MP2) computational methods. The chiral minima found are used to build homo- and heterochiral dimers. Six minima are found for the (PH2-PH2 )2 dimers and 27 for the (PH2-PHF)2 dimers. Pnicogen and hydrogen bonds, the non-covalent forces that stabilize the complexes, are characterized by Atoms in Molecules (AIM) and Natural Bond Orbital (NBO) methodologies. Those with several pnicogen bonds are more stable than those with hydrogen bonds. The chirodiastaltic energies amount to a total of 1.77 kJ mol(-1) for the Ra:Ra versus Ra:Sa (PH2-PH2 )2 dimers, 0.81 kJ mol(-1) for the RSa:RSa versus RSa:SRa (PH2-PHF)2 dimers, and 2.93 kJ mol(-1) for the RRa:RRa versus RRa:SSa (PH2-PHF)2 dimers. In the first and second cases, the heterochiral complex is favored whereas in the third case, the homochiral complex is favored.