Atoms-in-Molecules Dual Parameter Analysis of Weak to Strong Interactions: Behaviors of Electronic Energy Densities versus Laplacian of Electron Densities at Bond Critical Points

A DFT study of pyrrole-isoxazole derivatives as chemosensors for fluoride anion

The interactions between chemosensors, 3-amino-5-(4,5,6,7-tetrahydro-1H-indol-2-yl)isoxazole-4-carboxamide (AIC) derivatives, and different anions (F(-) Cl(-), Br(-), AcO(-), and H(2)PO(4) (-)) have been theoretically investigated using DFT approaches. It turned out that the unique selectivity of AIC derivatives for F(-) is ascribed to their ability of deprotonating the host sensors. Frontier molecular orbital (FMO) analyses have shown that the vertical electronic transitions of absorption and emission for the sensing signals are characterized as intramolecular charge transfer (ICT). The study of substituent effects suggests that all the substituted derivatives are expected to be promising candidates for fluoride chemosensors both in UV-vis and fluorescence spectra except for derivative with benzo[d]thieno[3,2-b]thiophene fragment that can serve as ratiometric fluorescent fluoride chemosensor only.

Hypervalent nonbonded interactions of a divalent sulfur atom. Implications in protein architecture and the functions

In organic molecules a divalent sulfur atom sometimes adopts weak coordination to a proximate heteroatom (X). Such hypervalent nonbonded S···X interactions can control the molecular structure and chemical reactivity of organic molecules, as well as their assembly and packing in the solid state. In the last decade, similar hypervalent interactions have been demonstrated by statistical database analysis to be present in protein structures. In this review, weak interactions between a divalent sulfur atom and an oxygen or nitrogen atom in proteins are highlighted with several examples. S···O interactions in proteins showed obviously different structural features from those in organic molecules (i.e., π(o) → σ(s)* versus n(o) → σ(s)* directionality). The difference was ascribed to the HOMO of the amide group, which expands in the vertical direction (π(o)) rather than in the plane (n(o)). S···X interactions in four model proteins, phospholipase A₂ (PLA₂), ribonuclease A (RNase A), insulin, and lysozyme, have also been analyzed. The results suggested that S···X interactions would be important factors that control not only the three-dimensional structure of proteins but also their functions to some extent. Thus, S···X interactions will be useful tools for protein engineering and the ligand design.

The nature of the interaction of organoselenium molecules with diiodine

The electronic structure of charge-transfer complexes of organoselenium compounds with diiodine has been studied at several levels of theory (Hartree-Fock, second order Møller-Plesset, and density functional theory). The complexation energies, optimized geometries, and the topology of the electron density and its Laplacian distribution, including domain averaged properties, have been analyzed. Special attention was paid to the influence of basis set superposition error on the energy of complexation. A tendency of organoselenium molecules to form more covalent intermolecular bonds with electron acceptors than with nitrogen atoms or other conventional electron donors has been revealed. The changes in atomic charges under complexation follow the main trends expected for the charge transfer. By means of the interacting quantum atoms (IQA) approach it has been found that the Se···I interaction is dominated by its quantum mechanical exchange-correlation contribution, the electrostatic interaction having a minor, repulsive role. IQA data have also been used to explain the value of the Se···I-I valence angle, as well as the topological charges on the iodine atoms in the complexes studied.

The low spin Co(II) fragment with homoleptic 1,10-phenanthroline ligands: synthesis, structures, DFT investigations, and magnetic properties

Two complexes {[Co(II)(phen)(3)][Co(III)(phen)(CN)(4)](2)}·phen·11H(2)O (1) and [Co(II)(μ-CN)(2)(Co(III))(2)(phen)(4)(CN)(6)]·C(2)H(5)OH·2H(2)O (2) were synthesized with identical starting materials but with a different order of addition. Their crystal structures, spectroscopic analysis, DFT calculations, and investigations of their magnetic properties are reported herein. The X-ray diffraction studies reveal that complex 1 mainly consists of discrete [Co(II)(phen)(3)](2+) cations and [Co(III)(phen)(CN)(4)](-) anions, while complex 2 is dominantly comprised of discrete neutral V-shaped trinuclear units [Co(II)(μ-CN)(2)(Co(III))(2)(phen)(4)(CN)(6)]. The first low-spin Co(II) fragment with homoleptic 1,10-phenanthroline ligands in 1 is observed at room temperature, owing to charge transfer from the neighboring anion via adventitious contacts and anion-π interactions. This is verified by structures, detailed theoretical analyses concerning frontier molecular orbital energy differences and Mulliken charge variations of the N atoms within the Co(II)N(6) sphere, and magnetism. Meanwhile, these kinds of supramolecular interactions are not found in complex 2, so it shows the ordinary magnetic behavior of the high-spin Co(II) ion. Our investigations highlight that for quantitative comprehension of spin-state energetic ordering in transition metal complexes, the supramolecular interactions must be taken into account in addition to classical ligand field theory. Moreover, we find that the [Co(II)(phen)(3)](2+) dication is sensitive to its surroundings in the solid state, which is beneficial for magnetic adjustment for the further synthesis of tunable molecular magnets and spin crossover systems.

Computational study of proper and improper hydrogen bonding in methanol complexes

The bulk properties of alcohols, like those of aqueous solutions, are governed mostly by hydrogen bonding; however, in contrast with water molecules, the chemical structure of a simple alcohol such as methanol offers an opportunity to explore the effects of both proper and improper hydrogen bonding on a single hydrogen donor. The presence of the hydroxyl group generally gives rise to a strong proper hydrogen bond, while the methyl group of methanol is likely involved in the weaker improper hydrogen bond, among other weak non-covalent interactions. The effects of the two types of hydrogen bonds on the stability, geometric parameters, and properties of electron density of methanol complexes are examined while considering different geometrical arrangements of the methanol dimer and the binary complexes of methanol with water, acetonitrile, and chloromethane. Subsequently, potential conclusions about the nature of improper hydrogen bonding and the origin of the C–H bond contraction that results upon complex formation are discussed. Quantum theory of atoms in molecules and natural bond orbital methods were used in the analysis; all calculations were performed at the MP2(full)/6-311++G(d,p) level of theory.

Dynamic behaviors of interactions: application of normal coordinates of internal vibrations to AIM dual functional analysis

A method to evaluate the dynamic nature of interactions is proposed based on the AIM dual functional analysis. Normal coordinates of internal vibrations (NIV) are employed to generate the perturbed structures necessary for the analysis. H(b)(r(c)) are plotted versus H(b)(r(c))-V(b)(r(c))/2 [= (variant Planck's over 2pi(2)/8m)nabla(2)rho(b)(r(c))] at bond critical points for the purpose. The plots are represented by the polar (R, theta) coordinate. Each plot for an interaction shows a specific curve, which is expressed by (theta(p), kappa(p)): theta(p) corresponds to the tangent line for the plot from the y-direction, and kappa(p) is the curvature. Although (R, theta) values correspond to the static nature of interactions, (theta(p), kappa(p)) values show the dynamic nature. The applicability of NIV is examined exemplified by the charge-transfer interactions as the first step to analyze the dynamic behaviors of interactions with NIV. The (theta(p), kappa(p)) values evaluated with NIV are very close to those obtained by the partial-optimization method (POM), where the distances or angles in question are fixed suitably, if the internal vibrations are substantially located on the interactions in question. The magnitudes of differences in theta(p) and kappa(p) between those evaluated with NIV and POM are < or = 2 degrees and < or = 2 au(-1), respectively, for usual interactions. The treatment is demonstrated to be applicable to a wide range of interactions.

A preliminary investigation of the additivity of pi-pi or pi+-pi stacking and T-shaped interactions between natural or damaged DNA nucleobases and histidine

Previous computational studies have examined pi-pi and pi(+)-pi stacking and T-shaped interactions in nucleobase-amino acid dimers, yet it is important to investigate how additional amino acids affect these interactions since simultaneous contacts often appear in nature. Therefore, this paper investigates the geometries and binding strengths of amino acid-nucleobase-amino acid trimers, which are compared to the corresponding nucleobase-amino acid dimer interactions. We concentrate on systems containing the natural nucleobase adenine or its (cationic) damaged counterpart, 3-methyladenine, and the aromatic amino acid histidine, in both the neutral and protonated forms. This choice of molecules provides information about pi-pi and pi(+)-pi stacking and T-shaped interactions in asymmetric, biologically relevant systems. We determined that both stacked and T-shaped interactions, as well as both pi-pi and pi(+)-pi interactions, exhibit geometric additivity. To investigate the energetic additivity in our trimers, the synergy (E(syn)) and the additivity (E(add)) energy were examined. E(add) reveals that it is important to consider the interaction between the two amino acids when examining the additivity of nucleobase-amino acid interactions. Additionally, E(syn) and E(add) indicate that pi(+)-pi interactions are quite different from pi-pi interactions. The magnitude of E(add) is generally less than 2 kJ mol(-1), which suggests that these interactions are additive. However, the interaction energy analysis does not provide information about the individual interactions in the trimers. Therefore, the quantum theory of atoms in molecules (QTAIM) was implemented. We find inconsistent conclusions from our QTAIM analysis and interaction energy evaluation. However, the magnitudes of the differences between the dimer and trimer critical point properties are extremely small and therefore may not be able to yield conclusive descriptions of differences (if any) between the dimer and trimer interactions. We hypothesize that, due to the limited number of investigations of this type, it is currently unclear how QTAIM can improve our understanding of pi-pi and pi(+)-pi dimers and trimers. Therefore, future work must systematically alter the pi-pi or pi(+)-pi system to definitively determine how the geometry, symmetry, and system size alter the QTAIM analysis, which can then be used to understand biologically relevant complexes.

Polar coordinate representation of Hb(rc) versus (h2/8m)nabla2rhob(rc) at BCP in AIM analysis: classification and evaluation of weak to strong interactions

Polar coordinate (R, theta) representation is proposed for the plot of Hb(rc) versus (h2/8m)nabla2rhob(rc) in AIM analysis to classify, evaluate, and understand weak to strong interactions in a unified way and in more detail; Hb(rc) and nabla2rhob(rc) are total electron energy densities and the Laplacian of rhob(rc) at bond critical points (BCPs: rc), respectively, where rhob(rc) are electron densities at rc. Both the x- and y-axes of the plot are expressed in the common unit of energy since Hb(rc) = Gb(rc) + Vb(rc) and (h2/8m)nabla2rhob(rc) = Hb(rc) - Vb(rc)/2 (= Gb(rc) + Vb(rc)/2), where Gb(rc) and Vb(rc) are kinetic energy densities and potential energy densities, respectively. Data employed for the plot are calculated at BCPs for full-optimized structures and optimized structures with the fixed distances (r) of r = r(o) + wa(o), where r(o) are the full-optimized distances, a(o) is the Bohr radius, and w = +/-0.1 and +/-0.2. The plot draws a helical stream starting from near origin (Hb(rc) = (h2/8m)nabla2rhob(rc) = 0) for very weak interactions and turns to the right as interactions become stronger. The helical stream is well described by the polar coordinate representation with (R, theta); R is given in the energy unit, and theta in degrees is measured from the y-axis. The ratio of Vb(rc)/Gb(rc) (= k) controls theta, of which an acceptable range in the plot is 45.0 < theta < 206.6 degrees. Each plot for an interaction gives a curve, which supplies important information. It is expressed by theta(p) and kappa(p); theta(p) corresponds to the tangent line measured from the y-direction, and kappa(p) is the curvature of the plot at w = 0. The polar coordinate (R, theta) representation with (theta(p), kappa(p)) helps us to classify, evaluate, and understand the nature of weak to strong interactions in a unified way.

Evidence for effective p(Z)-pi(Ar) conjugations (Z = S, Se, and Te, as well as Z = O) in 9-(arylchalcogenyl)triptycenes: experimental and theoretical investigations

The p(Z)-pi(Ar) conjugations must operate fully in the ground states of 9-(arylchalcogenyl)triptycenes (p-YC(6)H(4)ZTpc:1 (Z = O), 2 (Z = S), 3 (Z = Se), and 4 (Z = Te)), where the p-YC(6)H(4) group is placed in the bisected area between two phenyl planes of the triptycyl group with the parallel orientation. The ground-state geometries, which we call (A: pl), are confirmed by X-ray analysis. However, the conjugations never operate in the transition states between (A: pl) and/or the topomeric structures (A': pl'), where the Z-C(Tpc) bond is perpendicular to the plane. The site-exchange processes correlate to the conjugations. Temperature-dependent (1)H NMR spectra are analyzed for 2 and 3 to demonstrate the effective p(Z)-pi(Ar) conjugations. The activation energies for the interconversion between (A: pl) and (A': pl') (GR: gear process) were obtained for 2 (DeltaG(GR)(2)) and 3 (DeltaG(GR)(3)). DeltaG(GR)(3) correlate well with DeltaG(GR)(2), and DeltaG(GR)(2) are well analyzed by the Hammett-type dual parameters. DeltaG(GR)(2) and DeltaG(GR)(3) are demonstrated to be controlled by the resonance interaction of the p(Z)-pi(C(6)H(4))-p(Y) conjugations. QC calculations are performed on the ground and exited states of 1-4, which clarify the effective p(Z)-pi(C(6)H(4))-p(Y) conjugations for Z of heavier atoms.

Intramolecular apical metal-H-Csp3 interaction in molybdenum and silver complexes

The reaction of HTIMP3 (HTIMP3=tris[1-diphenylphosphino)-3-methyl-1H-indol-2-yl]methane) with AgBF4 and Mo(CO)3(NCCH3)3 leads to Ag(HTIMP3)BF4 and Mo(CO)3(HTIMP3), respectively. The metal centre is coordinated to the three phosphorus atoms of the HTIMP3 ligand, which adopts a facial coordination mode, placing a H-Csp3 hydrogen atom at the apical position close to the metal centre. The solid-state structure of Mo(CO)3(HTIMP3) has been determined by X-ray crystallography, and the data have been used as input parameters for obtaining the optimised geometry of the complex using the B3PW91 functional. The silver structure has been modelled from the X-ray parameters of the molybdenum structure. In addition, theoretical calculations on the H-Csp3 downfield shift upon metal coordination has also been performed. They reproduce the experimental H-Csp3 chemical shifts well and supports that proton deshielding is mainly due to the presence of the metal, since the hydrogen is already located in the cone created by the aromatic-phosphino arms in the free ligand.