Bond Critical Point Properties Research Articles

Towards universal substituent constants: Parameterizing bond critical point properties with electronegativity descriptors

AbstractThe properties of substituents have long been quantified by their effect elsewhere in a molecule. Ideally, intrinsic properties detailing the true properties of a substituent would be used. These properties are ideally transferable between molecules, to be robust and applied in different situations. Through a study on the bond critical point (BCP) properties of 117 substituents and 17 substrates we find that BCP properties from the quantum theory of atoms in molecules are not transferable between different bonded atoms. However, a substituent's changing electronegativity between substrates help quantify the observed variation. The relationship between changing electronegativities and critical point properties enables development of a relationship to predict critical point properties between a substituent and a new substrate, using only the electronegativity of a substituent attached to hydrogen, and the critical point property between the substituent and H.

A theoretical study on 1H-indole-2,3-dione complexes with lithium, sodium, and potassium cations.

A comparative study of the change in different properties of electronic and structural of the free 1H-indole-2,3-dione molecule and its complexes has been obtained. HOMA analysis was performed to investigate the effects of lithium sodium and potassium cations on the aromaticity of lithium sodium and potassium complexes of 1H-indole-2,3-dione. Several 1H-indole-2,3-dione complexes with lithium, sodium, and potassium cations were optimized at the B3LYP/6-311G(d,p) level. The cation and π interaction has been investigated from different aspects, including interaction energy calculations, charge transfer values, and changes in the aromaticity of the ring upon complexation. The charge transfer and natural population analysis for the complexes were performed with the natural bond orbital (NBO) analysis. The properties of bond critical points in complexes were studied by applying the quantum theory of atoms in molecules (QTAIM). Finally, the aromaticity change of phenyl induced upon complex formation was evaluated by applying the harmonic oscillator model of aromaticity (HOMA). [Li-INa]+ and [[Li-INb]+ were optimized with the wB97XD function using a version of Grimme's D2 dispersion model, and the absorption energy was compared with the calculation made with the B3LYP functional.

DFT-based study on the differences between odd and even Cn (n = 6–31) ring clusters

The gas-phase Cn (n = 6–31) carbocyclic clusters were systematically investigated based on DFT using ABCluster software. In this work, two geometrical parameters, degree of circularity and the ratio of carbon atoms occupying the fitted circle, were defined for the geometrical circle formed by Cn (n = 6–31) carbocyclic by curve-fitting the coordinates of the carbon atoms, and it is found that even-numbered carbon rings are always more rounded than odd-numbered ones. The study of relative stability of Cn ring clusters, on the one hand, revealed that even carbon rings are always more stable than odd ones. On the other hand, it proved that cyclic shape carbon clusters are always more stable than cage-like structure ones. In addition, the density of states, simulated electron absorption spectra, polarization response to electrostatic field, π-electron population, and topological properties of bond critical points were compressively studied. This work effectively filled the lack of research on odd-numbered carbocycles, a member of the carbocyclic family, and showed readers the physical and chemical reasons for the relative deformation of odd-numbered carbocycles.

Exploring Solid‐State Supramolecular Architectures of Penta(carboxymethyl)diethylenetriamine: Experimental Observation and Theoretical Studies

AbstractCrystals of penta(carboxymethyl)diethylenetriamine have been structurally characterized through single‐crystal X‐ray diffraction analysis. X‐ray diffraction analysis reveals that various non‐covalent interactions combine to determine the crystal packing and final solid‐state supramolecular assembling behavior. The title compound exhibited various 2D supramolecular networks generated through O−H⋅⋅⋅O and C−H⋅⋅⋅O interactions. The C−H⋅⋅⋅O interactions are pivotal in building a two‐dimensional framework, whose formation is readily analyzed with zero‐dimensional centrosymmetric dimeric rings as building blocks within the structure. All the intermolecular interactions are quantified through Hirshfeld surface analysis and fingerprint plots. Energy frameworks are constructed to analyze the dominant interaction energy involved in molecular packing strength. Bader's quantum theory of “atoms‐in‐molecules” (QTAIM) has been used to analyze and characterize non‐covalent interactions. The QTAIM analysis validates the existence of hydrogen bonding contacts, and the topological properties of bond critical points (BCPs), such as the electron density ρ(r) and its Laplacian ∇2ρ(r), are presented to correlate with the interaction energy. The topological analysis revealed that all of the interactions are closed‐shell interactions. Finally, the “Non‐covalent Interaction” (NCI) plot index illustrates the solid‐state supramolecular networks.

Toward universal substituent constants: Model chemistry sensitivity of descriptors from the quantum theory of atoms in molecules.

The quantum theory of atoms in molecules (QTAIM) provides a theoretical foundation to determine the properties of functional groups through additive atomic contributions. Many studies have used QTAIM in their analyses with a variety of electronic structure methods, but it is unknown if the properties measured using one model chemistry, the combination of the electronic structure method and basis set, can be compared to those measured by another. Here, we evaluate the sensitivity of QTAIM functional group and bond critical point properties using six functionals and seven basis sets. High-level B2PLYPD3-BJ/aug-cc-pV5Z reference values are provided for 116 functional groups and the property sensitivity with respect to these values are evaluated based on absolute deviations and by assessing linear relationships. Functional group properties, including charges, dipoles, quadrupoles and volumes, were found to be mostly insensitive to choice of computational model chemistry. However, due to structural and topological inconsistencies, the 6-31G(d) basis set is not recommended for use. Bond critical point properties varied with choice of model chemistry, but models incorporating hybrid functionals and triple-ζ basis sets provided values suitable for use in regression studies.

Structure, bonding and spectroscopic characterization of yttrium (III) octanoyl-aminocarboxylates complexes: A DFT study

This paper reports a theoretical study of yttrium (III) complexes with acylamino carboxylate ligands (N-octanoyl-alaninates, N-octanoyl-phenylalaninate, N-octanoyl-serinates) (Y(oct-ala)3, Y(oct-phe)3, Y(oct-ser)3). The calculations by density functional theory (DFT) suggest that the acylaminocarboxylate ligands act as a chelating bidentate ligand to the yttrium ions, and the coordination number was six. The reasonable agreement between theoretical and experimental IR, 1H NMR and UV-Vis spectra data provides a strong support to the theoretical structure and optical absorption properties of yttrium complexes. Atoms in molecules (AIM) theory was used to calculate the topological properties of bond critical points. The ▽2ρ and ρc values are in the range of 0.2587–0.2991 and 0.0512–0.0519, respectively, illustrating closed-shell interactions between ligands and yttrium ions. The values of bond degree (BD) were calculated to evaluate the strength of interactions. The results suggest that H(oct-phe) ligand interacts more strongly with Y3+.

Computational Rationalization of the Interaction of Fe(CO)4 and Substituted Benzyne Ligands

This study investigates the effect of different substituents on the interactions between Fe(CO)4 and substituted benzynes (C6X4, X = H, F, Cl, Br, CN, Me) in Fe(CO)4(η2-C6X4) complexes using MPW1PW91-based quantum mechanical calculations. In this respect, the study evaluates the influence of electron withdrawing and donating groups on the Fe-Cbenzyne bond distances and topological properties. In addition, the frontier orbital analysis is used to illustrate the electronic structure of complexes, and the percentage composition in terms of the defined groups of frontier orbitals is evaluated. To obtain insights into the physical nature of Fe-Cbenzyne bonds, we extensively use the energy decomposition analysis (EDA) and Bader’s Quantum Theory of Atoms-in-Molecules (QTAIM). To this end, in addition to the examination of the properties of bond critical points, we apply the Pendas interacting quantum atoms (IQA) scheme, which enables a rigorous and physical study of Fe-Cbenzyne bonds in these complexes. Also, electron localization function (ELF) and localized-orbital locator (LOL) calculations are used to illustrate Fe-C bonds in the investigated complexes.

Computational rationalization of the interaction of Fe(CO)4 and substituted benzyne ligands

This study investigates the effect of different substituents on the interactions between Fe(CO)4 and substituted benzynes (C6X4, X = H, F, Cl, Br, CN, Me) in Fe(CO)4(η2-C6X4) complexes using MPW1PW91-based quantum mechanical calculations. In this respect, the study eva­luates the influence of electron withdrawing and donating groups on the Fe—Cbenzyne bond distances and topological properties. In addition, the frontier orbital analysis is used to illustrate the electronic structure of complexes, and the percentage composition in terms of the defined groups of frontier orbitals is evaluated. To obtain insights into the physical nature of Fe—Cbenzyne bonds, we extensively use the energy decomposition analysis (EDA) and Bader's Quantum Theory of Atoms-in-Molecules (QTAIM). To this end, in addition to the examination of the properties of bond critical points, we apply the Pendas interacting quantum atoms (IQA) scheme, which enables a rigorous and physical study of Fe—Cbenzyne bonds in these complexes. Also, electron localization function (ELF) and localized-orbital locator (LOL) calculations are used to illustrate Fe—C bonds in the investigated complexes.

Intermolecular Interactions in Ionic Crystals of Nucleobase Chlorides—Combining Topological Analysis of Electron Densities with Energies of Electrostatic Interactions

Understanding intermolecular interactions in crystals of molecular ions continues to be difficult. On the one hand, the analysis of interactions from the point of view of formal charges of molecules, similarly as it is commonly done for inorganic ionic crystals, should be performed. On the other hand, when various functional groups are present in the crystal, it becomes natural to look at the interactions from the point of view of hydrogen bonding, π…π stacking and many other kinds of non-covalent atom–atom bonding. Often, these two approaches seem to lead to conflicting conclusions. On the basis of experimental charge densities of cytosinium chloride, adeninium chloride hemihydrate, and guanine dichloride crystals, with the help of theoretical simulations, we have deeply analysed intermolecular interactions among protonated nucleobases, chloride anions and water molecules. Here, in the second paper of the series of the two (Kumar et al., 2018, IUCrJ 5, 449–469), we focus on applying the above two approaches to the large set of dimers identified in analysed crystals. To understand electrostatic interactions, we analysed electrostatic interaction energies (Ees) computed directly from molecular charge densities and contrasted them with energies computed only from net molecular charges, or from a sum of electric multipolar moments, to find the charge penetration contribution to Ees. To characterize non-covalent interactions we performed topological analyses of crystal electron densities and estimated their interaction energies (EEML) from properties of intermolecular bond critical points. We show that the overall crystal architecture of the studied compounds is governed by the tight packing principle and strong electrostatic attractions and repulsions between ions. Many ions are oriented to each other in a way to strengthen attractive electrostatic interactions or weaken strong repulsion, but not all of them. Numerous bond critical points and bond paths were found between ions, including nucleobase cations despite their overall repulsive interactions. It is clear there is no correlation between EEML and Ees. However, strong relation between EEML and the charge penetration component of Ees is observed. The relation holds regardless of interaction types or whether or not interacting molecules bear the same or opposite charges. Thus, a charge density-based approach for computing intermolecular interaction energies and the atom–atom approach to analyse non-covalent interactions do complement each other, even in ionic systems.

Can halogen bond energy be reliably estimated from electron density properties at bond critical point? The case of the (A)nZ—Y•••X− (X, Y = F, Cl, Br) interactions

AbstractRelationships between the Y•••X bond critical point (BCP) properties or the Y•••X distance and the halogen bond interaction energy were analyzed in detail by theoretical methods for the series of structures [(A)nZ—Y•••X]− (X,Y = F, Cl, Br; totally 441 structures). No relationship was found for the whole set of structures or for the series [(A)nZ—F•••X]−, [(A)nZ—Cl•••X]−, and [(A)nZ—Br•••X]−. The interaction energies may be roughly estimated from the BCP properties for the series [(A)nZ—Y•••F]−, [(A)nZ—Y•••Cl]−, and [(A)nZ—Y•••Br]− as well as for [(A)nZ—Y•••X]− (when (A)nZ is variable, X and Y are constant) with the mean absolute deviation values 2.04‐4.38 kcal/mol. The corresponding recommended relationships are provided and they are significantly different from the popular dependencies deduced previously for other types of noncovalent interactions. Tremendous effect of the computational method and basis set on the relationships under analysis was discovered. Computational results clearly indicate that, for practical purposes, the Eint(BCP property) dependencies should be established not simply for each global type of interactions (hydrogen bond, halogen bond, chalcogen bond, etc.) but for each combination of the first and second order atoms taking into account also the computational method and basis set.

Influences of the substituents on the Cr=C bond in [(OC)5Cr=C(OEt)-para-C6H4X] complexes: quantum Theory of Atoms in Molecules, Energy Decomposition Analysis, and Interacting Quantum Atoms

This study was conducted to investigate the effect of various substituents on the Cr=C bond in the [(OC)5Cr=C(OEt)-para-C6H4X] complexes using B3LYP*-based quantum mechanical calculations. In this respect, the study evaluates the influence of electron withdrawing and donating groups on the Cr=C bond distances and topological properties and correlates the calculated parameters with the Hammett and Brown constants for the para-substituted (σp and σ p + , respectively) functional groups. Also, the frontier orbital analysis was used to show the electronic structure of complexes and the percentage composition in terms of the defined groups of frontier orbitals was evaluated. To obtain insight into the physical nature of Cr=C bond bonds, we extensively used energy decomposition analysis and Bader’s Quantum Theory of Atoms-in-Molecules (QTAIM). With this aim, in addition to examining the bond critical points properties, we apply Pendas’ Interacting Quantum Atoms (IQA) scheme, which enables the rigorous and physical study of Cr=C bonds in these complexes.

Behaviors and interactions of H2 absorption to CuRn+

Behaviors of H2-absorption to CuRn+ have been investigated at the CCSD(T) theoretical level. The “T-shaped” H2-absorption to the Cu or to Rn atom can be found with different binding energies, and it can be characterized by infrared radiation spectrum. The three-atom Cu/Rn⋯H2 interactions are investigated by AIM theory, topological analysis on electron density function, delocalization index, and independent gradient model analysis. It characterizes the partial covalent character for the Cu⋯H2 interactions and van der Waals character for the Rn⋯H2 interactions. Consistencies show the reliability of bond critical point properties for the present three-atom Cu/Rn⋯H2 interactions due to the very small HH distances.

The QTAIM Approach to Chemical Bonding in Triruthenium Carbonyl Cluster: [Ru3 (μ-H)(μ3-κ2-Haminox-N,N)(CO)9

The bonding in the hydride triruthenium carbonyl cluster [Ru3 (μ-H)(μ3-κ2-Haminox-N,N)(CO)9 is investigated by using the Quantum Theory of Atoms-in-Molecules (QTAIM). Calculated metal–metal and metal–ligand bond critical points (bcp) properties, electron density ρ(b), Laplacian ∇2ρ(b), local energy density H(b), local kinetic (Lagrangian) energy density G(b), local potential energy density V(b) ellipticity ε(b), and bond delocalization indices δ(A, B) are consistent with the relevant transition metal clusters in the literature. The topological data recognizes bond paths (bp) and bond critical points for metal-metal interactions in the core of the hydride triruthenium cluster [Ru(1)-Ru(3) and Ru(2)-Ru(3)]. However, no direct bond path is found for the interaction between the hydride bridged Ru atoms, while a non-negligible delocalization index δ(Ru(1)…Ru(2)) is obtained for this non-bonding interaction. An interaction of 5-center 6-electron type is proposed for the core. The topological parameters of Ru-N oxazoline ring bond suggest a pure σ-bond.

Degradation of Glyphosate by Mn-Oxide May Bypass Sarcosine and Form Glycine Directly after C-N Bond Cleavage.

Glyphosate is the active ingredient of the common herbicide Roundup. The increasing presence of glyphosate and its byproducts has raised concerns about its potential impact on the environment and human health. In this research, we investigated abiotic pathways of glyphosate degradation as catalyzed by birnessite under aerobic and neutral pH conditions to determine whether certain pathways have the potential to generate less harmful intermediate products. Nuclear magnetic resonance (NMR) spectroscopy and high-performance liquid chromatography (HPLC) were utilized to identify and quantify reaction products, and density functional theory (DFT) calculations were used to investigate the bond critical point (BCP) properties of the C-N bond in glyphosate and Mn(IV)-complexed glyphosate. We found that sarcosine, the commonly recognized precursor to glycine, was not present at detectable levels in any of our experiments despite the fact that its half-life (∼13.6 h) was greater than our sampling intervals. Abiotic degradation of glyphosate largely followed the glycine pathway rather than the AMPA (aminomethylphosphonic acid) pathway. Preferential cleavage of the phosphonate adjacent C-N bond to form glycine directly was also supported by our BCP analysis, which revealed that this C-N bond was disproportionately affected by the interaction of glyphosate with Mn(IV). Overall, these results provide useful insights into the potential pathways through which glyphosate may degrade via relatively benign intermediates.

Theoretical investigation on the covalence in AgRnX and XAgRn (X = F - I).

CCSD(T) calculations were performed to investigate the stabilities and interaction mechanisms of the AgRnX and XAgRn (X = F - I) series. Dissociation energies and frontier orbital properties demonstrate an increased trend of stabilities. Ag spd hybrids and Rn/X sp hybrids come into the σAg-Rn and σAg-X bonding orbital. The nature of Ag-Rn, Ag-X and Rn-X interactions were investigated by atoms in molecules (AIM) theory. The negative energy density and positive Laplacian values, as well as small electron densities at bond critical points (BCPs), characterize the moderate strength with partial covalence of interactions. BCP properties (-G/V and G/ρ), electron density deformations and natural resonance theory (NRT) results display increased covalence down the periodic table.

Correlation of bond metallicity measures to electronegativity for binary oxides

AbstractWe have investigated alkali, alkaline‐earth, and rutile binary oxides within density functional theory (DFT) and Bader's atoms‐in‐molecules theory, focusing on properties of bond and ring critical points, and their relations to band gap and Pauling electronegativity. We find linear relations of kinetic energy density, electron density, and the gap divided by kinetic energy density at the bond critical points to the difference of Pauling electronegativities of the cation and oxygen anion. At the ring critical points of rutile compounds, we also find that some bond metallicity measures are linearly related to the difference of electronegativities. This study extends our knowledge about the relations between bond critical points, band gap, and electronegativity, but also shows for the first time a quantitative relation between quantities at the ring critical points and global properties of the compounds.

Stabilities and interactions of CuRnX and XCuRn (X = F – I): ab initio calculations

ABSTRACTTheoretical investigations on the CuRnX and XCuRn (X = F – I) series have been performed at the CCSD(T) theoretical level. Analyses on dissociation energy and frontier orbital show a decreased trend of stabilities down the periodic table. NBO analyses show the existence of σCu-Rn and σCu-X bonding orbital resulted from the overlap between Cu spd hybrid and Rn/X sp hybrid. The Cu–Rn, Cu–X and Rn–X interactions characterised by negative energy density values, positive Laplacian values and small electron densities at bond critical point (BCP) can be described as interactions of moderate strength with partial covalence. Analyses on electron localisation functions, electron density deformations, BCP properties (−G/V and G/ρ) and natural resonance theory demonstrate an increased covalence down the periodic table.

Theoretical Charge Density Analysis and Nonlinear Optical Properties of Quasi-Planar 1-Aryl(hetaryl)-5-phenylpent-1-en-4-yn-3-ones

The topological features of intermolecular bonding have been investigated by theoretical charge density analysis of six crystalline 1-aryl(hetaryl)-5-phenylpent-1-en-4-yn-3-ones. The energies of intermolecular interactions have been estimated from intermolecular bond critical point properties. The molecules crystallize in three supramolecular synthons through 2–6 C–H···O═C interactions, and the binding energy was found to be characteristic for each synthon and comparable to that of a single O–H···O hydrogen bond. Comparison of C–H···O bonding at quasi-planar pentenynones, chalcones, and polyenones allowed making suggestions about a possible synthetic route to acentric materials with nonlinear optical properties based on these molecules.

Crystal chemistry of the kieserite–cobaltkieserite solid solution, Mg1-xCox(SO4)·H2O: well-behaved oddities

Earlier independent crystal-structure studies of kieserite, Mg(SO 4 )·H 2 O, and the isotypic transition-metal compounds Me 2+ (SO 4 )·H 2 O (Me 2+ = Mn, Fe, Co, Ni, Zn) indicated that the lattice parameters of kieserite are significantly larger than expected from both the respective ionic radii and the octahedral Mg/Me–O bond lengths. This volume mismatch was especially noticeable in comparison to the respective (high-spin) Co 2+ compound with its only slightly larger ionic radius than Mg. In order to study this possible discrepancy, we synthesized several members of the kieserite–cobaltkieserite solid solution series, Mg 1− x Co x (SO 4 )·H 2 O, and investigated the structures of ten representatives, including the end-members, using consistent single-crystal X-ray diffraction data. The present results confirm the supposed anomaly, showing a significant negative correlation of polyhedral vs . unit-cell volumes, which both change in total by ± 1.2 A 3 over the series ( V kies . = 356.0, V Co-kies . = 354.8 A 3 ; = 2.078, = 2.097 A). This effect is realized by folding and rotations within the polyhedral assemblage, apparently driven by angular O–Me–O and especially Me–O–S/Me changes. Apart from this oddity, the Mg 1− x Co x (SO 4 )·H 2 O solid solution can be described as ‘well-behaved’, i.e. no indications for miscibility gaps or cation ordering effects were found, and cell parameters and other structural data behave according to Vegard’s law in linear relation with the refined Mg 1− x Co x content. Explanations for the paradoxical volume behaviour of kieserite compared to cobaltkieserite (and other transition-metal kieserites) are probably related to the absence, respectively presence of partly filled 3 d orbitals and/or to well-established differences in electronegativity. Literature data on bond critical point properties of forsterite and transition-metal olivines indicate that the bond critical point r c lies significantly closer to Mg as compared to the transition cations, which might be ascribed in part to the absence of d orbitals at the Mg atom. In turn, the respective mutual influence on the electron density at the oxygen atoms in case of Mg–O bonds could represent a relevant modifier for the second coordination sphere and thus contribute to the paradoxical crystal chemical behaviour observed for kieserite as compared to isotypic transition-metal compounds in general and to cobaltkieserite in particular.

Metal-Metal Bonding in Uranium-Group 10 Complexes.

Heterobimetallic complexes containing short uranium–group 10 metal bonds have been prepared from monometallic IUIV(OArP-κ2O,P)3 (2) {[ArPO]− = 2-tert-butyl-4-methyl-6-(diphenylphosphino)phenolate}. The U–M bond in IUIV(μ-OArP-1κ1O,2κ1P)3M0, M = Ni (3–Ni), Pd (3–Pd), and Pt (3–Pt), has been investigated by experimental and DFT computational methods. Comparisons of 3–Ni with two further U–Ni complexes XUIV(μ-OArP-1κ1O,2κ1P)3Ni0, X = Me3SiO (4) and F (5), was also possible via iodide substitution. All complexes were characterized by variable-temperature NMR spectroscopy, electrochemistry, and single crystal X-ray diffraction. The U–M bonds are significantly shorter than any other crystallographically characterized d–f-block bimetallic, even though the ligand flexes to allow a variable U–M separation. Excellent agreement is found between the experimental and computed structures for 3–Ni and 3–Pd. Natural population analysis and natural localized molecular orbital (NLMO) compositions indicate that U employs both 5f and 6d orbitals in covalent bonding to a significant extent. Quantum theory of atoms-in-molecules analysis reveals U–M bond critical point properties typical of metallic bonding and a larger delocalization index (bond order) for the less polar U–Ni bond than U–Pd. Electrochemical studies agree with the computational analyses and the X-ray structural data for the U–X adducts 3–Ni, 4, and 5. The data show a trend in uranium–metal bond strength that decreases from 3–Ni down to 3–Pt and suggest that exchanging the iodide for a fluoride strengthens the metal–metal bond. Despite short U–TM (transition metal) distances, four other computational approaches also suggest low U–TM bond orders, reflecting highly transition metal localized valence NLMOs. These are more so for 3–Pd than 3–Ni, consistent with slightly larger U–TM bond orders in the latter. Computational studies of the model systems (PH3)3MU(OH)3I (M = Ni, Pd) reveal longer and weaker unsupported U–TM bonds vs 3.