Semilocalized approach to investigation of chemical reactivity

Application of the power series for the one‐electron density matrix 36 to the case of two interacting molecules is shown to yield a semilocalized approach to investigate chemical reactivity, which is characterized by the following distinctive features: (1) Electron density (ED) redistributions embracing orbitals of the reaction centers of both molecules and of their neighboring fragments are studied instead of the total intermolecular interaction energy; (2) the ED redistributions are expressed directly in the basis of fragmental orbitals (FOs) without passing to the basis of delocalized molecular orbitals (MOs) of initial molecules; (3) terms describing the ED redistributions due to an intermolecular contact arise as additive corrections to the purely monomolecular terms and thereby may be analyzed independently; (4) local ED redistributions only between orbitals of the reaction centers of both molecules are described by lower‐order terms of the power series, whereas those embracing both the reaction centers and their neighborhoods are represented by higher‐order terms. As opposed to the standard perturbative methods based on invoking the delocalized (canonical) MOs of isolated molecules, the results of the approach suggested are in‐line with the well‐known intuition‐based concepts of the classic chemistry concerning reactivity, namely, with the assumption about different roles of the reaction center and of its neighborhood in a chemical process, with the expectation about extinction of the indirect influence of a certain fragment (substituent) when its distance from the reaction center grows, etc. Such a parallelism yields quantum chemical analogs for the classic concepts and thereby gives an additional insight into their nature. The scope of validity of these concepts also is discussed. Applicability of the approach suggested to specific chemical problems is illustrated by a brief consideration of the S_N2 and Ad_E2 reactions. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 302–316, 2003     

Natural bond orbital analysis of some S‐nitrosothiols biological molecules

Theoretical study of several S‐nitrosothiols biological molecules has been performed using quantum computational ab initio RHF and density functional B3LYP and B3PW91 methods with 6‐31G(d,p) basis set. Geometries obtained from DFT calculations were used to perform natural bond orbital (NBO) analysis. It is noted that the weakness in the S? N sigma bond is due to n_O1→σ delocalization and is responsible for the longer S? N bond length in S‐nitrosothiols. It is also noted that decreased occupancy of the localized σ_SN orbital in the idealized Lewis structure or increased occupancy of σ of the non‐Lewis orbital, and their subsequent impact on molecular stability and geometry (bond lengths) are related with the resulting p character of the corresponding sulfur natural hybrid orbital of σ_SN bond orbital. In addition, the charge transfer energy decreases with the increasing of the Hammett constants of substituent groups, and the partial charge distribution on the skeletal atoms shows that the electrostatic repulsion or attraction between atoms can give a significant contribution to the intramolecular and intermolecular interaction. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

A comparative study of some lithium and hydrogen‐bonded complexes: Ab initio and QTAIM studies

The nature of the interactions of cyanide with lithium and hydrogen halides was investigated using ab initio calculations and topological analysis of electron density. The computed properties of the lithium‐bonded complexes RCN···LiX (R = H, F, Cl, Br, C?CH, CH?CH₂, CH₃, C₂H₅; X = Cl, Br) were compared with those of corresponding hydrogen‐bonded complexes RCN···HX. The results show that both types of intermolecular interactions are “closed‐shell” noncovalent interactions. The effect of substitution on the interaction energy and electron density at the bond critical points of the lithium and hydrogen bonding interactions is similar. In comparison, the interaction energies of lithium‐bonded complexes are more negative than those of hydrogen‐bonded counterparts. The electrostatic interaction plays a more important role in the lithium bond than in the hydrogen bond. On complex formation, the net charge and energy of the Li atom decrease and the atomic volume increases, while the net charge and energy of the H atom increase and the atomic volume decreases. © 2013 Wiley Periodicals, Inc.     

Generalized population analysis of three‐center two‐electron bonding

Modern valence bond theory, in its spin‐coupled (SC) form, is used to assess the utility of generalized population analysis, using correlated density matrices, for identifying patterns of three‐center two‐electron bonding in B₂H₆, B₃H, and CH₂Li₂. The effect on the relevant three‐center indices of including electron correlation, via the SC method, is assessed by means of comparison with analogous Hartree–Fock values. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Pure through‐bond state in organic molecules for analysis of the relationship between intramolecular interactions and total energy

Ab initio configuration interaction through‐space/bond interaction analysis was proposed for the examination of specific intramolecular interactions including the effect of electron correlations. To test the effectiveness of our method, we applied it to rotational barrier in ethane. The results of our test suggest that the insensitivity of the ethane barrier to geometric relaxations is intimately connected with the cancellation of interactions through orbital overlaps and other factors. The orbital overlaps include exchange repulsion and hyperconjugation; other factors include classic Coulomb interaction and changes in bond orbital energy. The rotational state without the barrier (pure through‐bond state) can be achieved by deleting not only the “vicinal” interactions between the C? H bonds that belong to different methyl groups but also the “geminal” interactions within the methyl groups. Our mixing analysis of molecular orbitals supports the superiority of the staggered conformer by hyperconjugation. Moreover, it was demonstrated that our treatment could be applied to excited states as well as to the ground state, including electron correlation effects. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

Charge-Flow Profiles along Curvilinear Paths: A Flexible Scheme for the Analysis of Charge Displacement upon Intermolecular Interactions

The Charge-Displacement (CD) analysis has proven to be a powerful tool for a quantitative characterization of the electron-density flow occurring upon chemical bonding along a suitably chosen interaction axis. In several classes of interesting intermolecular interactions, however, an interaction axis cannot be straightforwardly defined, and the CD analysis loses consistency and usefulness. In this article, we propose a general, flexible reformulation of the CD analysis capable of providing a quantitative view of the charge displacement along custom curvilinear paths. The new scheme naturally reduces to ordinary CD analysis if the path is chosen to be a straight line. An implementation based on a discrete sampling of the electron densities and a Voronoi space partitioning is described and shown in action on two test cases of a metal-carbonyl and a pyridine-ammonia complex.     

Theoretical Studies on the Hydrogen‐bonding and π‐Stacking Interactions in the m‐Nisoldipine Polymorphism Dimers

The intermolecular interactions in the dimers of m‐nisoldipine polymorphism were studied by B3LYP calculations and quantum theory of "atoms in molecules" (QTAIM) studies. Four geometries of dimers were obtained: dimer I (a‐dimer, O···H? N), dimer II (b‐dimer, O···H? N), dimer III (b‐dimer, π‐stacking‐c), and dimer IV (b‐dimer, π‐stacking‐p). The interaction energies of the four dimers are along the sequence of II>I>III>IV. The intermolecular distance of the interactions follows the order: I (O···H? N)II>III>IV, and the electrostatic character decreases along the sequence: I>II>III>IV.     

Natural bond orbital‐based energy density analysis for correlated methods: Second‐order Møller–Plesset perturbation and coupled‐cluster singles and doubles

Natural bond orbital‐based energy density analysis (NBO‐EDA), which split energies into atomic and bonding contributions, is proposed for correlated methods such as coupled‐cluster singles and doubles (CCSD) and second‐order Møller–Plesset (MP2) perturbation. Applying NBO‐EDA for CCSD and MP2 to ethylene and the Diels–Alder reaction, we are successful in obtaining useful knowledge regarding electron correlation of π‐ and σ‐type orbitals, and clarifying the difference of the reaction barriers and heat of reaction calculated by CCSD and MP2. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Two-electron integrations in the quantum theory of atoms in molecules with correlated wave functions

A recent method proposed to compute two-electron integrals over arbitrary regions of space [Martin Pendas, A. et al., J Chem Phys 2004, 120, 4581] is extended to deal with correlated wave functions. To that end, we use a monadic factorization of the second-order reduced density matrix originally proposed by E. R. Davidson [Chem Phys Lett 1995, 246, 209] that achieves a full separation of the interelectronic components into one-electron terms. The final computational effort is equivalent to that found in the integration of a one determinant wave function with as many orbitals as occupied functions in the correlated expansion. Similar strategies to extract the exchange and self-interaction contributions from the two-electron repulsion are also discussed, and several numerical results obtained in a few test systems are summarized.     

A computational study on the ring stretching modes of halogen‐substituted pyridine involved in H‐bonding

Density functional method B3LYP plus the AUG‐cc‐pVDZ and AUG‐cc‐pVTZ basis sets is used to investigate ring normal modes of halogen‐substituted pyridines involved in the N ··· H? X H‐bonds with HX (X = F, Cl). The results demonstrated that the formation of hydrogen bond leads to an increase in the frequencies of the ring breathing mode v₁, the N‐para‐C stretching mode v_6a and the meta‐CC stretching mode v_8a, whereas there is no change in the triangle mode v₁₂ for free pyridine and a smaller blue shift for substituted pyridines. There is a strong coupling between the C? Y stretching vibration and the triangle mode (ortho‐ and para‐substituted) or the breathing mode (meta‐substituted) in substituted pyridines, which leads to the frequency decrease in the triangle or breathing modes. The natural bond orbital analysis suggests that electrostatic interaction and charge transfer caused by the intermolecular and intramolecular hyperconjugations are the origin of the frequency blue shift in the ring stretching modes. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Theoretical investigation on charge‐assisted halogen bonding interactions in the complexes of bromocarbons with some anions

A series of dimeric complexes formed between bromocarbon molecules and two anions (Br^? and CN^?) have been investigated by using MP2 method. The quantum theory of atoms in molecules (QTAIM) and the second‐order perturbation natural bond orbital (NBO) approaches were applied to analyze the electron density distributions of these complexes and to explore the nature of charge‐assisted halogen bonding interactions. As anticipated, these interactions are significantly stronger relative to the corresponding neutral ones. The results derived from ab initio calculations described herein reveal a major contribution from the electrostatic interaction on the stability of the systems considered. Beside the electrostatic interaction, the charge‐transfer force and the second‐order orbital interaction also play an important role in the formation of the complexes, as a NBO analysis suggested. The presence of halogen bonds in the complexes has been identified in terms of the QTAIM methodology, and several linear relationships have been established to provide more insight into charge‐assisted halogen bonding interactions. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

One‐, two‐, and three‐electron bonding: An “in vitro” theoretical study using noninteger nuclear charges evidences the crucial role of electronegativity in the strength of symmetrical bonds

Fictitious hydrogen atoms H*_A of variable nuclear charge 0.5 ≤ Z_A ≤ 2 (and thus of variable electronegativity) are used to study the intrinsic dependency of chemical bonding on electronegativity. Dissociation energy and equilibrium distance are reported for symmetrical 1‐, 2‐ and 3‐electron H*_AH*_A systems and 2‐electron dissymmetrical H*_A‐H ones. Dealing with symmetrical systems, the strongest two‐electron bonds are found for Z_A ≈ 1.2. Oneelectron and three‐electron strongest bonds occur respectively with low (ca. 0.7) and high (ca. 1.7) Z_A values and can become stronger than the corresponding 2‐electron system. Comparison with data on real systems leads to conclude that electronegativity is a prevailing atomic property in the control of the dissociation energy of symmetrical 1‐, 2‐ and 3‐electron bonds. A simplified mathematical model at Hartree‐Fock or Heitler‐London level with a minimal basis set reproduces these trends semi‐quantitatively and provides the overall shape of the dissociation curves. Finally some points are qualitatively discussed from MO analysis, which emphasize the dependence of the bonding/antibonding properties on the nucleus charge Z_A and their occupancy number. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Three‐dimensional networks containing rectangular Sr4 and Ba4 units: Synthesis,structure, bonding,and potential application for Ne gas separation

New porous three‐dimensional metal‐organic frameworks are synthesized that contain infinite chains of Sr_n and Ba_n rectangles. Their structures are elucidated by means of spectroscopic techniques such as nuclear magnetic resonance and Fourier transform infrared, and the respective crystal structures are determined. The electronic structure of basic units of the crystals are computed using density functional theory at the B3LYP/6‐31G(d,p)/def2‐TZVP level, and the bonding and reactivity are analyzed using natural bond orbital analysis, the quantum theory of atoms in molecules, and conceptual density functional theory. The possibilities of noble gas (Ng) storage inside the crystal structures are explored through modeling a Ng atom inside the frozen geometry of the crystal. It was found that a neon atom can fit into a cavity in the Sr and Ba crystal structures whereas other Ngs (He, Ar, Kr) exhibit repulsive interactions with the crystal structure. Ab initio molecular dynamics simulations for up to 500 fs at 77 and 298 K suggest that the structures incorporating a neon atom are kinetically stable. © 2015 Wiley Periodicals, Inc.     

Probing the weakest bond and the cleavage of p‐chlorobenzaldehyde diperoxide energetic molecule via quantum chemical calculations and theoretical charge density analysis

A high‐level ab initio Hartree‐Fock/Møller‐Plesset 2 and density functional theory quantum chemical calculations were performed on p‐chlorobenzaldehyde diperoxide energetic molecule to understand its bond topological, electrostatic, and energetic properties. The optimized molecular geometry for the basis set 6‐311G** exhibit chair diperoxide ring and planar aromatic side rings. Although the diperoxide ring bear same type of side rings, surprisingly, both the rings are almost perpendicular to each other, and the dihedral angle is 96.1°. The MP2 method predicts the O? O bond distance as ～1.466 Å. The charge density calculation reveals that the C? C bonds of chlorobenzaldehyde ring have rich electron density and the value is ～2.14 e Å^?3. The maximum electron density of the O? O bonds does not lie along the internuclear axes; in view of this, a feeble density is noticed in the ring plane. The high negative values of laplacian of C? C bonds (approximately ?22.4 e Å^?5) indicate the solidarity of these bonds, whereas it is found too small (approximately ?1.8 e Å^?5 for MP2 calculation) in O? O bonds that shows the existence of high degree of bond charge depletion. The energy density in all the C? C bonds are found to be uniform. A high electronegative potential region is found at the diperoxide ring which is expected to be a nucleophilic attack area. Among the bonds, the O? O bond charge is highly depleted and it also has high bond kinetic energy density; in consequence of this, the molecular cleavage is expected to happen across these bonds when the material expose to any external stimuli such as heat or pressure treatment. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Fluoride anion sensing mechanism of a BODIPY‐linked hydrogen‐bonding probe

The sensing mechanism of a fluoride‐anion probe BODIPY‐amidothiourea ( 1c ) has been elucidated through the density functional theory (DFT) and time‐dependent density functional theory (TDDFT) calculations. The theoretical study indicates that in the DMSO/water mixtures the fluorescent sensing has been regulated by the fluoride complex that formed between the probe 1c /two water molecules and the fluoride anion, and the excited‐state intermolecular hydrogen bond (H‐B) plays an important role in the fluoride sensing mechanism. In the first excited state, the H‐Bs of the fluoride complex 1cFH₂ are overall strengthened, which induces the weak fluorescence emission. In addition, molecular orbital analysis demonstrates that 1cFH₂ has more obvious intramolecular charge transfer (ICT) character in the S₁ state than 1cH₂ formed between the probe 1c and two water molecules, which also gives reason to the weaker fluorescence intensity of 1cFH₂ . Further, our calculated UV‐vis absorbance and fluorescence spectra are in accordance with the experimental measurements. © 2018 Wiley Periodicals, Inc.