Cooperativity in Hydrogen-Bonded Interactions: Ab Initio and “Atoms in Molecules” Analyses

Substituted fullerenes as a promising capping ligand towards stabilization of exohedral Dy(III) based single-ion magnets: a theoretical study

Organometallic dysprosocenium-based molecular magnets are the forefront runners in offering giant magnetic anisotropy and blocking temperatures close to the boiling point of liquid nitrogen. Attaining linearity in the organometallic dysprosocenium complexes is the key to generating giant magnetic anisotropy and blocking barriers. In the present study, we have unravelled the coordination ability of the substituted fullerene (C55X5)- (where X = CCH3, B, and N) generated by fencing around the five-membered ring of fullerene towards stabilizing a new family of exohedral dysprosium organometallic complexes showcasing giant magnetic anisotropy and blockade barriers. Eight exohedral mononuclear dysprosium organometallic complexes, namely [Dy(η5-C55X5)(η4-C4H4)] (1), [Dy(η5-C55X5)(η5-Cp)]+ (2), [Dy(η5-C55X5)(η5-Cp*)]+ (3), [Dy(η5-C55X5)(η6-C6H6)]2+ (4), [Dy(η5-C55X5)(η8-C8H8)] (5), [Dy(η5-C55X5)2]+ (6) (where X = CCH3), [Dy(η5-C55B5)2]+ (7) and [Dy(η5-C55N5)2]+ (8), were studied using scalar relativistic density functional theory (SR-DFT) and the complete active space self-consistent field (CASSCF) methodology to shed light on the structure, stability, bonding and single-ion magnetic properties. SR-DFT calculations predict complexes 1-8 to be highly stable, with a strictly linear geometry around the Dy(III) ion in complexes 6-8. Energy Decomposition Analysis (EDA) predicts the following order for interaction energy (ΔEint value): 5 > 1 > 2 ≈ 3 > 6 > 7 > 8 > 4, with sizable 4f-ligand covalency in all the complexes. CASSCF calculations on complexes 1-8 predict stabilization of mJ |±15/2〉 as the ground state for all the complexes except for 5, with the following trend in the Ucal values: 6 (1573 cm-1) ≈ 3 (1569 cm-1) > 1 (1538 cm-1) > 8 (1347 cm-1) > 2 (1305 cm-1) > 7 (1284 cm-1) > 4 (1125 cm-1) > 5 (108 cm-1). Ab initio ligand field theory (AILFT) analysis provides a rationale for Ucal ordering, where π-type 4f-ligand interactions in complexes 1-4 and 6-8 offer giant barrier height while the large (C8H8)2- rings generate δ-type interaction in 5, which diminishes the axiality in the ligand field. Our detailed finding suggests that the exohedral organometallic dysprosocenium complexes are more linear compared to bent [DyCp*2]+ cations and display a giant barrier height exceeding 1500 cm-1 with negligible quantum tunnelling of magnetization (QTM) - a new approach to design highly anisotropic dysprosium organometallic complexes.

Cooperativity between Intermolecular Hydrogen and Carbon Bonds in ZY···CH3CN/CH3NC···HX Trimers (ZY = H2O, H2S, HF, HCl, HBr, NH3, and H2CO; HX = HF, HCl, and HBr)

Hydrogen-bonding and carbon-bonding interactions are widespread in nature. We studied the cooperativity between these interactions in 42 trimeric complexes ZY···CH3CN/CH3NC···HX, where ZY molecules are H2O, H2S, HF, HCl, HBr, NH3, and H2CO, and HX molecules are HF, HCl, and HBr. Acetonitrile (CH3CN) and isoacetonitrile (CH3NC) act as hydrogen bond acceptors as well as carbon bond donors in these trimers. Various theoretical methods, such as electronic structure calculations, quantum theory of atoms in molecule (QTAIM), natural bond orbital (NBO), and reduced density gradient analysis, are employed to study these trimers, and the results are compared with the corresponding ZY···CH3CN/CH3NC and CH3CN/CH3NC···HX dimers. Electronic structure calculations are performed at the second-order Mo̷ller-Plesset perturbation theory using the 6-311++G(2d,2p) basis set. We show that both the interactions act synergistically in these trimers leading to an increase in their bond strength as compared to the strength in the individual dimers. The cooperative energies for these trimers are in the range of 0.69 to 3.22 kJ/mol. It is seen that the carbon bonds benefit more from the cooperativity than the hydrogen bonds. The trends of cooperativity and correlations of interaction energies and cooperative energies with relevant QTAIM and NBO parameters are reported.

Unravelling performance of honeycomb structures as drug delivery systems for the isoniazid drug using DFT-D3 correction dispersion and molecular dynamic simulations

In this study, the potential of aluminum nitride (h-AlN), boron nitride (h-BN) and silicon carbide (h-SiC) nanosheets as the drug delivery systems (DDS) of isoniazid (INH) was scrutinized through density functional theory (DFT) and molecular dynamic (MD) simulations. We performed DFT periodic calculations on the geometry and electronic features of nanosheets adsorbed with INH by the DFT functional (DZP/GGA-PBE) employed in the SIESTA code. In the energetically favorable model, an oxygen atom of the C-O group of the INH molecule interacts with a Si atom of the h-SiC at 2.077 Å with an interaction energy of -1.361 eV. Charge transfer (CT) calculation by employing the Mulliken, Hirshfeld and Voronoi approaches reveals that the monolayers and drug molecules act as donors and acceptors, respectively. The density of states (DOS) calculations indicate that the HOMO-LUMO energy gap (HLG) of the h-SiC nanosheet declines significantly from 2.543 to 1.492 eV upon the adsorption of the INH molecule, which causes an electrical conductivity increase and then produces an electrical signal. The signal is linked to the existence of INH, demonstrating that h-SiC may be an appropriate sensor for INH sensing. The decrease in HLG for the interaction of INH and h-SiC is the uppermost (up to 41%) representing the uppermost sensitivity, whereas the sensitivity trend is σ(h-SiC) > σ(h-AlN) > σ(h-BN). Quantum theory of atoms in molecules (QTAIM) investigations is employed to scrutinize the nature of the INH/nanosheet interactions. The QTAIM analysis reveals that the interaction of the INH molecule and h-SiC has a partially covalent nature, while INH/h-AlN model electrostatic interaction occurs in the system and noncovalent and electrostatic interaction for the INH/h-BN model. Finally, the state-of-the-art DFT-MD simulations utilized in this study can mimic ambient conditions. The results obtained from the MD simulation show that it takes more time to bond the INH drug and h-SiC, and the INH/h-SiC system becomes stable. The results of the current research demonstrate the potential of h-SiC as a suitable sensor and drug delivery platform for INH drugs to remedy tuberculosis.

DFT-D3 and TD-DFT Studies of the Adsorption and Sensing Behavior of Mn-Phthalocyanine toward NH3, PH3, and AsH3 Molecules

This study employs density functional theory (DFT) calculations at the B3LYP/6-311+g(d,p) level to investigate the interaction of XH3 gases (X = N, P, As) with the Mn-phthalocyanine molecule (MnPc). Grimme's D3 dispersion correction is applied to consider long-range interactions. The adsorption behavior is explored under the influence of an external static electric field (EF) ranging from -0.514 to 0.514 V/Å. Chemical adsorption of XH3 molecules onto the MnPc molecule is confirmed. The adsorption results in a significant decrease in the energy gap (Eg) of MnPc, indicating the potential alteration of its optical properties. Quantum theory of atoms in molecules (QTAIM) analysis reveals partially covalent bonds between XH3 and MnPc, and the charge density differenc (Δρ) calculations suggest a charge donation-back donation mechanism. The UV-vis spectrum of MnPc experiences a blue shift upon XH3 adsorption, highlighting MnPc's potential as a naked-eye sensor for XH3 molecules. Thermodynamic calculations indicate exothermic interactions, with NH3/MnPc being the most stable complex. The stability of NH3/MnPc decreases with increasing temperature. The direction and magnitude of the applied electric field (EF) play a crucial role in determining the adsorption energy (Eads) for XH3/MnPc complexes. The Eg values decrease with an increasing negative EF, which suggests that the electrical conductivity (σ) and the electrical sensitivity (ΔEg) of the XH3/MnPc complexes are influenced by the magnitude and direction of the applied EF. Overall, this study provides valuable insights into the suggested promising prospects for the utilization of MnPc in sensing applications of XH3 gases.

Characteristics of nonconventional hydrogen bonds and stability of dimers of chalcogenoaldehyde derivatives: a noticeable role of oxygen compared to other chalcogens

In this work, twenty-four stable dimers of RCHZ with R = H, F, Cl, Br, CH3 or NH2 and Z = O, S, Se or Te were determined. It was found that the stability of most dimers is primarily contributed by the electrostatic force, except for the dominant role of the induction term in those involving a Te atom, which has been rarely observed. Both electron-donating and -withdrawing groups in substituted formaldehyde cause an increase in the strength of nonconventional Csp2-H⋯Z hydrogen bonds, as well as the dimers, in which the electron donating effect plays a more crucial role. The strength of nonconventional hydrogen bonds decreases in the following order: Csp2-H⋯O ≫ Csp2-H⋯S > Csp2-H⋯Se > Csp2-H⋯Te. Remarkably, a highly significant role of the O atom compared to S, Se and Te in increasing the Csp2-H stretching frequency and strength of the nonconventional hydrogen bonds and dimers is found. A Csp2-H stretching frequency red-shift is observed in Csp2-H⋯S/Se/Te, while a blue-shift is obtained in Csp2-H⋯O. When Z changes from O to S to Se and to Te, the Csp2-H blue-shift tends to decrease and eventually turns to a red-shift, in agreement with the increasing order of the proton affinity at Z in the isolated monomer. The magnitude of the Csp2-H stretching frequency red-shift is larger for Csp2-H⋯Te than Csp2-H⋯S/Se, consistent with the rising trend of proton affinity at the Z site and the polarity of the Csp2-H bond in the substituted chalcogenoaldehydes. The Csp2-H blue-shifting of the Csp2-H⋯O hydrogen bonds is observed in all dimers regardless of the electron effect of the substituents. Following complexation, the electron-donating derivatives exhibit a stronger Csp2-H blue-shift compared to the electron-withdrawing ones. Notably, the stronger Csp2-H blue-shift turns out to involve a less polarized Csp2-H bond and a decrease in the occupation at the σ*(Csp2-H) antibonding orbital in the isolated monomer.

Computational study of the interactions of tetravalent actinides (An = Th-Pu) with the α-Fe13 Keggin cluster

In recent years, evidence has emerged that actinide (An) uptake at the enhanced actinide removal plant (EARP) at the UK's Sellafield nuclear site occurs via An interactions with an α-Fe13 Keggin molecular cluster during ferrihydrite formation. We here study theoretically the substitution of aquo complexes of the actinides Th-Pu onto a Na-decorated α-Fe13 Keggin cluster using DFT at the PBE0 level. The optimised Pu-O and Pu-Fe distances are in good agreement with experiment and Na/An substitutions are significantly favourable energetically, becoming more so across the early 5f series, with the smallest and largest ΔrG° being for Th and Pu at -335.7 kJ mol-1 and -396.0 kJ mol-1 respectively. There is strong correlation between the substitution reaction energy and the ionic radii of the actinides (Δrε0R2 = 0.97 and ΔrG° R2 = 0.91), suggesting that the principal An-Keggin binding mode is ionic. Notwithstanding this result, Mulliken and natural population analyses reveal that covalency increases from Th-Pu in these systems, supported by analysis of the occupied Kohn-Sham molecular orbitals where enhanced An(5f)-O(2p) overlap is observed in the Np and Pu systems. By contrast, quantum theory of atoms in molecules analysis shows that U-Keggin binding is the most covalent among the five actinides, in keeping with previous studies.

The Missing Chalcogen Bonding Donor: Strongly Polarized Oxygen of Water

A biscyclen molecular cabin, synthesized by connecting two cyclen macrocycles with four linkages, entraps a Li+···H2O···Li+ trimer with a water molecule clamped by two Li+ ions. This configuration results in strongly polarized water, characterized by a water proton resonance shift of up to 10.00 ppm. The arrangement facilitates unprecedented O-centered chalcogen bonds between the lone pairs of pyridinyl nitrogen atoms and polarized water oxygen, as confirmed by X-ray crystallography, NMR spectroscopy, and theoretical calculations. Further observation of O-centered chalcogen bonding in a H2O·(LiCl)2 cluster suggests its widespread presence in hydrated salt systems.

Wolfium bonds in homodimers of MX4Y (M = Mo, W; X = F, Cl, Br; Y = O, S, Se)

The term "wolfium bond" has been recently introduced to describe the noncovalent attraction between an atom of group 6 and a nucleophile via a σ-hole binding site. Crystal structures commonly contain a motif wherein two MX4Y units are arranged in close proximity, where M represents either Mo or W, and X and Y refer to halogen and chalcogen atoms respectively. DFT calculations were thus applied to a wide range of homodimers of these molecules so as to assess their preferred arrangements, and to characterize the types of bonding that are present in each in a systematic manner. The most stable Dual-X configuration is symmetric and contains a pair of equivalent M⋯X bonds. The interaction energies range from -8 to -29 kcal mol-1, and are largest for X = F, Y = O, and M = W. The X electron donor is replaced by Y, and the two wolfium bonds are reduced to one, in the less stable Mono-Y structure, with interaction energies between -2 and -10 kcal mol-1. There is some question as to whether the weaker bonds of this type constitute true wolfium bonds.

The radical scavenging activity of monocaffeoylquinic acids: the role of neighboring hydroxyl groups and pH levels

Caffeoylquinic acids (CQAs) are well-known antioxidants. However, a key aspect of their radical scavenging activity - the mechanism of action - has not been addressed in detail thus far. Here we report on a computational study of the mechanism of activity of CQAs in scavenging hydroperoxyl radicals. In water at physiological pH, the CQAs demonstrated ≈ 104 times higher HOO˙ antiradical activity than in lipid medium (k(lipid) ≈ 104 M-1 s-1). The activity in the aqueous solution was determined by the hydrogen transfer mechanism of the adjacent hydroxyl group (O6'-H) of the dianion states (Γ = 93.2-95.2%), while the single electron transfer reaction of these species contributed 4.8-6.8% to the total rate constants. The kinetics estimated by the calculations are consistent with experimental findings in water (pH = 7.5), yielding a kcalculated/kexperimental = 2.4, reinforcing the reliability and precision of the computational method and demonstrating its utility for evaluating radical reactions in silico. The results also revealed the pH dependence of the HOO˙ scavenging activity of the CQAs; activity was comparable for all compounds below pH 3, however at higher pH values 5CQA reacted with the HOO˙ with lower activity than 3CQA or 4CQA. It was also found that CQAs are less active than Trolox below pH 4.7, however over pH 5.0 they showed higher activity than the reference. The CQAs had the best HOO˙ antiradical activity at pH values between 5.0 and 8.6. Therefore, in the physiological environment, the hydroperoxyl antiradical capacity of CQAs exhibits similarity to renowned natural antioxidants including resveratrol, ascorbic acid, and Trolox.

M-Encapsulated Be12O12 Nano-Cage (M = K, Mn, or Cu) for CH2O Sensing Applications: A Theoretical Study

DFT and TD-DFT studies of B3LYP/6-31 g(d,p) with the D2 version of Grimme's dispersion are used to examine the adsorption of a CH2O molecule on Be12O12 and MBe12O12 nano-cages (M = K, Mn, or Cu atom). The energy gap for Be12O12 was 8.210 eV, while the M encapsulation decreased its value to 0.685-1.568 eV, whereas the adsorption of the CH2O gas decreased the Eg values for Be12O12 and CuBe12O12 to 4.983 and 0.876 eV and increased its values for KBe12O12 and MnBe12O12 to 1.286 and 1.516 eV, respectively. The M encapsulation enhanced the chemical adsorption of CH2O gas with the surface of Be12O12. The UV-vis spectrum of the Be12O12 nano-cage was dramatically affected by the M encapsulation as well as the adsorption of the CH2O gas. In addition, the adsorption energies and the electrical sensitivity of the Be12O12 as well as the MBe12O12 nano-cages to CH2O gas could be manipulated with an external electric field. Our results may be fruitful for utilizing Be12O12 as well as MBe12O12 nano-cages as candidate materials for removing and sensing formaldehyde gas.

A Comprehensive Study of the Radical Scavenging Activity of Rosmarinic Acid

Rosmarinic acid (RA) is reported in separate studies to be either an inducer or reliever of oxidative stress, and this contradiction has not been resolved. In this study, we present a comprehensive examination of the radical scavenging activity of RA using density functional theory calculations in comparison with experimental data. In model physiological media, RA exhibited strong HO• radical scavenging activity with overall rate constant values of 2.89 × 1010 and 3.86 × 109 M-1 s-1. RA is anticipated to exhibit excellent scavenging properties for HOO• in an aqueous environment (koverall = 3.18 × 108 M-1 s-1, ≈2446 times of Trolox) following the hydrogen transfer and single electron transfer pathways of the dianion state. The neutral form of the activity is equally noteworthy in a lipid environment (koverall = 3.16 × 104 M-1 s-1) by the formal hydrogen transfer mechanism of the O6(7,15,16)-H bonds. Chelation with RA may prevent Cu(II) from reduction by the ascorbic acid anion (AA-), hence blocking the OIL-1 pathway, suggesting that RA in an aqueous environment also serves as an OIL-1 antioxidant. The computational findings exhibit strong concurrence with the experimental observations, indicating that RA possesses a significant efficacy as a radical scavenger in physiological environments.

Toward functionalization of ZnO nanotubes and monolayers with 5-aminolevulinic acid drugs as possible nanocarriers for drug delivery: a DFT based molecular dynamic simulation

We have investigated the interactions between a 5-aminolevulinic acid (ALA) drug and ZnO nanostructures including ZnO monolayers and ZnO nanotubes (ZnONTs) using density functional theory (DFT) calculations. In the context of the dispersion corrected Perdew-Burke-Ernzerhof (PBE) approach, the energetics, charge transfer, electronic structure and equilibrium geometries have been estimated. As ALA is adsorbed onto/into the ZnONTs and on the ZnO monolayer with interaction energies (Eint) of -2.55/-2.75 eV and -2.51 eV, respectively, the calculated Eint values and bonding distances (∼2 Å) reveal that the interaction type is chemisorption. The ZnO nanostructures showed promising performance in the ALA drug functionalization, taking into account the interaction energy values. The band gap almost remains unchanged for both of the substrates under consideration after ALA adsorption, and the semiconductor properties of the substrates are preserved, according to the analyzed density of states (DOSs) spectra. The interaction nature of the ALA-ZnO nanostructures according to the atom in molecule (AIM) analysis was found to be polar attraction with partial covalent bonding between O and Zn. Our DFT based molecular dynamic (MD) simulation results demonstrate that, in the aqueous solution, ALA moves toward the interior sidewall of the ZnONTs and ZnO nanosheet surface and binds to the Zn atom through its O (carbonyl/hydroxyl groups) and N atoms and the hydroxyl H atom was dissociated and binds to the O atom of the ZnO surface. However, in the case of ALA adsorption onto the outer surface of ZnONTs, only the O atoms of carbonyl groups bind to the Zn atom and the structure of the drug remains undestroyed during the adsorption. The current findings shed light on the polar drug adsorption/encapsulation behavior on/into ZnO nanostructures, which may encourage further use of ZnO-based nanomaterials in the field of drug delivery and bio-functionalized nanomaterials.

Metal ion-decorated hexasilaprismane and its derivative as a molecular container for the separation of CO2 from flue gas molecules: a computational study

The electronic structure of hexasilaprismane (HSP) was examined with different computational techniques to elucidate the bonding features and the electrostatic surface potential of HSP. The carbon dioxide adsorption and separation capacities of metal-ion-decorated hexasilaprismane (HSP) were examined with DFT and CBS-QB3. Furthermore, the 1,2,3,4,5,6-hexaphenylprismasilane (HPPS) molecule was examined for its binding with metal ions and gas adsorption capacity. The Mg²⁺ ion complexed HPPS molecule adsorbs 15CO₂ molecules with an average binding free energy of -0.98 eV per molecule. The calculated gravimetric densities of 45.1 and 48.4 wt% show that these systems can be employed for CO₂ capture. The substantial difference in the affinity of the designed systems for CO₂ gas molecules compared to N₂ and CH₄ molecules show the potential of the systems for CO₂ separation from N₂ and CH₄ gas molecules.

Actinium coordination chemistry: A density functional theory study with monodentate and bidentate ligands

In the current study, the coordination chemistry of nine-coordinate Ac(III) complexes with 35 monodentate and bidentate ligands was investigated using density functional theory (DFT) in terms of their geometries, charges, reaction energies, and bonding interactions. The energy decomposition analysis with naturals orbitals for chemical valence (EDA-NOCV) and the quantum theory of atoms in molecules (QTAIM) were employed as analysis methods. Trivalent Ac exhibits the highest affinities toward hard acids (such as charged oxophilic donors, fluoride), so its classification as a hard acid is justified. Natural population analysis quantified the involvement of 5f orbitals on Ac to be about 30% of total valence electron natural configuration indicating that Ac is a member of the actinide series. Pearson correlation coefficients were used to study the pairwise correlations among the bond lengths, ΔG reaction energies, charges on Ac and donor atoms, and data from EDA-NOCV and QTAIM. Strong correlations and anticorrelations were found between Voronoi charges on donor atoms with ΔG, EDA-NOCV interaction energies and QTAIM bond critical point densities.

Halogen bond and polymorphism in trans-bis(2-iodo-5-halopyridine)dihalocopper(ii) complexes: crystallographic, theoretical and magnetic studies

As the halogen atom on position 5 of the 2I5YP ligand gets heavier the probability of crystallizing the syn-conformer increases; 2I5Cl-Cl crystallizes as the anti-conformer whereas 2I5Br-Cl crystallizes as syn- and anti-conformers.

Can the Fluxionality in Borospherene Influence the Confinement-Induced Bonding between Two Noble Gas Atoms?

A density functional theory study is performed to determine the stability and bonding in the neon dimer inside the B₃₀N₃₀ fullerene cage, the fluxional B₄₀ cage, and within non-fluxional cages such as B₁₂N₁₂ and C₆₀. The nature of bonding in the Ne₂ encapsulated B₄₀ is compared with the that in other cages in an attempt to determine whether any possible alterations are brought about by the dynamical nature of the host cage apart from the associated confinement effects. The bonding analysis includes the natural bond order (NBO), Bader's Atoms-in-Molecules electron density analysis (AIM), and energy decomposition analysis (EDA), revealing the non-covalent nature of the interactions between the Ne atoms and that between the Ne and the cage atoms. The formation of all the Ne₂@cage systems is thermochemically unfavourable, the least being that for the B₃₀N₃₀ cage, which can easily be made favourable at lower temperatures. The Ne-Ne distance is lowest in the smallest cage and increases as the cage size increase due to steric relaxation experienced by the dimer. The dynamical picture of the systems is investigated by performing ab initio molecular dynamics simulations using the atom-centred density matrix propagation (ADMP) technique, which shows the nature of the movement of the dimer inside the cages, and by the fact that since it moves as a single entity, a weak bonding force holds them together, apart from their proven kinetic stability.

Harnessing Greenhouse Gases Absorption by Doped Fullerenes with Externally Oriented Electric Field

In this work, a theoretical investigation of the effects caused by the doping of C20 with silicon (Si) atom as well as the adsorption of CO, CO2 and N2 gases to C20 and C19Si fullerenes was carried out. In concordance with previous studies, it was found that the choice of the doping site can control the structural, electronic, and energetic characteristics of the C19Si system. The ability of C20 and C19Si to adsorb CO, CO2 and N2 gas molecules was evaluated. In order to modulate the process of adsorption of these chemical species to C19Si, an externally oriented electric field was included in the theoretical calculations. It was observed that C19Si is highly selective with respect to CO adsorption. Upon the increase of the electric field intensity the adsorption energy was magnified correspondingly and that the interaction between CO and C19Si changes in nature from a physical adsorption to a partial covalent character interaction.

Investigation of the Nature of Intermolecular Interactions in Tetra(thiocyanato)corrolato-Ag(III) Complexes: Agostic or Hydrogen Bonded?

Tetra(thiocyanato)corrolato-Ag(III) complexes presented here constitute a new class of metallo-corrole complexes. The spectroscopic properties of these complexes are quite unusual and interesting. For example, the absorption spectra of these β-substituted corrolato-Ag(III) complexes are very different from those of the β-unsubstituted corrolato-Ag(III) derivatives. Single-crystal XRD analysis of a representative tetra(thiocyanato)corrolato-Ag(III) derivative reveals C-H···Ag interactions. The C-H···Ag interactions are rarely demonstrated in the crystal lattice of a discrete coordination/organometallic compound. Optimization of the hydrogen positions of the crystal structure discloses the geometrical parameters of the said interaction as a Ag···H distance of 2.597 Å and ∠C-H···Ag of 109.62°. The natural bond orbital analysis provides information about the donor-acceptor orbitals involved in the interactions and their interaction energies. It was observed that the σ_C-H orbital overlaps with the vacant d-orbital of Ag with an interaction energy of 17.93 kJ/mol. The filled d-orbital of Ag overlaps with the σ*_C-H orbital with an interaction energy of 4.79 kJ/mol. The highlights of this work are that the H···Ag distance is outside of the distance range for the typical agostic interaction but fitted with the weak H-bond distance. However, the ∠C-H···Ag angle is within the range of the agostic interaction. Both crystallographic data and electronic structure calculations reveal that these kinds of intermolecular interactions in square-planar d⁸ Ag(III) complexes are intermediate in nature. Thus, they cannot be categorically called either hydrogen bonding or agostic interaction.

Carbon-Centered Hydrogen Bonds in Proteins

Hydrogen bonding (H-bonding) without lone pair(s) of electrons and π-electrons is a concept developed 2-3 years ago. H-bonds involving less electronegative tetrahedral carbon are beyond the classical concept of H-bonds. Herein, we present the first report on H-bonds with tetravalent carbons in proteins. A special bonding arrangement is needed to increase the negative charge density around the sp³-hybridized carbon atom. Therefore, less electronegative elements such as As and Mg, when bonded to sp³-C, enable the C-atoms as H-bond acceptors. Careful protein structure analysis aided by several quantum chemical calculations suggests that these H-bonds are weak to moderate in strength. We developed an empirical equation to estimate the C-H···C H-bond energy in proteins from the distances between the C- and H-atoms. In proteins, the binding energies range from -5.4 to -14.0 kJ/mol. The C-H···C H-bonds assist the substrate binding in proteins. We also explored the potential role of these carbon-centered H-bonds in C-H bond activation through σ-bond metathesis. To our surprise, contribution from these H-bonds is almost of similar magnitude as that from C-H···π H-bonds for C-H bond activation.

Rubidium and caesium aluminyls: synthesis, structures and reactivity in C-H bond activation of benzene

Expanding knowledge of low valent aluminium chemistry, rubidium and caesium aluminyls are reported to complete the group 1 (Li-Cs) set of metal aluminyls. Both compounds crystallize as a contacted dimeric pair supported by M⋯π(arene) interactions with a pronounced twist between aluminyl units. Density functional theory calculations show symmetrical bonding between the M and Al atoms, with an Al centred lone-pair donating into vacant Rb and Cs orbitals. Interestingly, despite their structural similarity the Cs aluminyl enables C-H bond activation of benzene, but not the Rb aluminyl reflecting the importance of the alkali metal in these heterobimetallic systems.

Structural and molecular properties of complexes of biomolecules and metal-organic frameworks: dispersion-corrected DFT treatment

Investigation of complexes of nanostructured materials and biomolecules has attracted much attention by various researchers as it can contribute to coherent growth and extended application of nanostructures in different technologies. In this research, following a comprehensive approach, we examined the interaction between different amino acids and metal-organic frameworks (MOFs) at atomic scale using computational chemistry. For this purpose, we employed the density functional theory (DFT-D2) calculations to afford a molecular description of the interaction properties of the amino acids and MOF-5 by examining the interaction energy and the electronic structure of the amino acid/MOF complexes. We found strong interactions between the amino acids and MOF through their polar groups as well as aromatic rings in the gas phase. However, our findings were significantly different in solvent media, where water molecules prevent the amino acids from approaching the active sites of MOF, causing weak attractions between them. The evaluation of nature of interaction between the amino acids and MOF by the atoms-in-molecules (AIM) theory shows that the electrostatic attractions are the main force contributing to bond formation between the interacting entities. Furthermore, our DFT-PBE model of theory was validated against the comprehensive MP2 quantum level of theory.

Polymorphism and isomorphism in trans-bis(2,5-diiodopyridine)dihalocopper(ii) complexes: theoretical and crystallographic studies

Two conformational polymorphs of [Cu(25dIpy)2Cl2] have been prepared, the anti-polymorph crystallized from 2-propanol at room temperature (green) and the syn-polymorph crystallized from acetonitrile at 60 °C (brown).

Theoretical Aspects of Nonconventional Hydrogen Bonds in the Complexes of Aldehydes and Hydrogen Chalcogenides

Hydrogen bonds (H-bonds) in the complexes between aldehydes and hydrogen chalcogenides, XCHO...nH₂Z with X = H, F, Cl, Br, and CH₃, Z = O, S, Se, and Te, and n = 1,2, were investigated using high-level ab initio calculations. The C_sp2-H...O H-bonds are found to be about twice as strong as the C_sp2-H...S/Se/Te counterparts. Remarkably, the S/Se/Te-H...S/Se/Te H-bonds are 4.5 times as weak as the O-H...O ones. The addition of the second H₂Z molecule into binary systems induces stronger complexes and causes a positive cooperative effect in ternary complexes. The blue shift of C_sp2-H stretching frequency involving the C_sp2-H...Z H-bond sharply increases when replacing one H atom in HCHO by a CH₃ group. In contrast, when one H atom in HCHO is substituted with a halogen, the magnitude of blue-shifting of the C_sp2-H...Z H-bond becomes smaller. The largest blue shift up to 92 cm^-1 of C_sp2-H stretching frequency in C_sp2-H...O H-bond in CH₃CHO...2H₂O has rarely been observed and is much greater than that in the cases of the C_sp2-H...S/Se/Te ones. The C_sp2-H blue shift of C_sp2-H...Z bonds in the halogenated aldehydes is converted into a red shift when H₂O is replaced by a heavier analogue, such as H₂S, H₂Se, or H₂Te. The stability and classification of nonconventional H-bonds including C_sp2-H...Se/Te, Te-H...Te, and Se/Te-H...O have been established for the first time.

Theoretical assessments on the interaction between amino acids and the g-Mg3N2 monolayer: dispersion corrected DFT and DFT-MD simulations

The interaction of a few amino acids (AAs) with the graphene-like magnesium nitride (g-Mg₃N₂) monolayer has been investigated with density functional theory (DFT) simulations. The Mg site was found to cause significant attraction with the polar active sites of AAs. Such AAs, are capable of producing electrostatics bonding with -48.012 (kcal mol^-1) of interaction energy for tyrosine. The good consistency of the DFT interaction energy with the second-order Møller-Plesset method was found. Furthermore, the DFT-MD simulation of the tyrosine/g-Mg₃N₂ system demonstrated that this host-guest system is stable at ambient conditions. The electronic structures and quantum molecular descriptors were calculated, and the results revealed that the g-Mg₃N₂ monolayer is sensitive to the interaction with AAs. Our first-principles outcomes suggest comprehensive visions into the functionalization of g-Mg₃N₂, and anticipate its applicability as an unprecedented nanovector for AAs. In addition, g-Mg₃N₂ nanosheets can be utilized as biosensors for biomolecules detection. These are very hopeful for promising biological and pharmaceutical applications of g-Mg₃N₂.

Dihydrogen Activation by Lithium- and Sodium-Aluminyls

To date, aluminyl anions have been exclusively isolated as their potassium salts. We report herein the synthesis of the lithium and sodium aluminyls, M₂ [Al(NON^Dipp )]₂ (M=Li, Na. NON^Dipp =[O(SiMe₂ NDipp)₂ ]^2- ; Dipp=2,6-iPr₂ C₆ H₃ ). Both compounds crystallize from non-coordinating solvent as "slipped" contacted dimeric pairs with strong M⋅⋅⋅π(aryl) interactions. Isolation from Et₂ O solution affords the monomeric ion pairs (NON^Dipp )Al-M(Et₂ O)₂ , which contain discrete Al-Li and Al-Na bonds. The ability of the full series of Li, Na and K aluminyls to activate dihydrogen is reported.

Ionization of NO by superhalogens: DFT and QTAIM approaches

 Nitric oxide (NO) is a precursor to NO2, toxic gas, and a major air pollutant. Its ionization has been difficult due to its high ionization energy. We propose here the ionization of NO to NO+ using superhalogens. We study the interaction of NO with superhalogens (X = LiF2, BeF3 and, BF4) using DFT and QTAIM approaches, which lead to the formation of NO-X complexes. These complexes and their isomers are ionic with positively charged NO, which can be stabilized by two F–N bonds and F–O bonds, respectively. This reveals that NO can be ionized by electron transfer to superhalogens. The size of superhalogens has been noticed to play a crucial in the ionization of NO.

Actual Symmetry of Symmetric Molecular Adducts in the Gas Phase, Solution and in the Solid State

This review discusses molecular adducts, whose composition allows a symmetric structure. Such adducts are popular model systems, as they are useful for analyzing the effect of structure on the property selected for study since they allow one to reduce the number of parameters. The main objectives of this discussion are to evaluate the influence of the surroundings on the symmetry of these adducts, steric hindrances within the adducts, competition between different noncovalent interactions responsible for stabilizing the adducts, and experimental methods that can be used to study the symmetry at different time scales. This review considers the following central binding units: hydrogen (proton), halogen (anion), metal (cation), water (hydrogen peroxide).

CAl4Mg0/−: Global Minima with a Planar Tetracoordinate Carbon Atom

Isomers of CAl4Mg and CAl4Mg− have been theoretically characterized for the first time. The most stable isomer for both the neutral and anion contain a planar tetracoordinate carbon (ptC) atom. Unlike the isovalent CAl4Be case, which contains a planar pentacoordinate carbon atom as the global minimum geometry, replacing beryllium with magnesium makes the ptC isomer the global minimum due to increased ionic radii of magnesium. However, it is relatively easier to conduct experimental studies for CAl4Mg0/− as beryllium is toxic. While the neutral molecule containing the ptC atom follows the 18 valence electron rule, the anion breaks the rule with 19 valence electrons. The electron affinity of CAl4Mg is in the range of 1.96–2.05 eV. Both the global minima exhibit π/σ double aromaticity. Ab initio molecular dynamics simulations were carried out for both the global minima at 298 K for 10 ps to confirm their kinetic stability.

Two new canted antiferromagnetic systems: magnetic, theoretical, and crystallographic studies on trans-bis(2-iodopyridine)dihalocopper(ii)

The two complexes Cu(2ip)X₂ were prepared (where 2ip = 2-iodopyridine and X = Cl or Br), and their crystal structures were determined. The two complexes are isomorphous and form a magnetic chain based on the two-halide exchange pathway. The powder and single crystal magnetic susceptibility data were measured down to 1.8 K. The exchange is antiferromagnetic along the chain; the exchange is stronger in the bromide complex than in the corresponding chloride complex. In the ordered state, weak moments appear along some of the axes, indicative of spin-canting. The calculated spin densities and the mapped surface of spin density on total electron density were used to rationalize qualitatively the observed magnetic behavior. Low temperature structures are compared with the room temperature data; the C-IX-Cu and Cu-XX-Cu distances are shorter at low temperatures; in contrast, the covalent bonds of the organic ligand (2-iodopyridine) are longer (negative thermal expansion of the covalent bonds). The anomalous behavior is rationalized using charge transfer from Cu-X group to the anti-bonding orbital of the organic ligand. Quantum theory of atoms in molecules was used to analyze C-IX halogen bonding interactions.

Covalency in AnCl3 (An = Th-No)

The geometric and electronic structures of AnCl3 are studied computationally using scalar relativistic, hybrid density functional theory (PBE0). The An-Cl bond lengths generally decrease across the 5f series, although there is a slight lengthening from Fm-Cl to No-Cl as the metal ions display increasing M(ii) character. Covalency in the An-Cl bond is studied using a wide range of metrics drawn from the Natural Bond Orbital, Natural Resonance Theory and Quantum Theory of Atoms-in-Molecules (QTAIM) methods, including bond order, orbital composition, orbital overlap and electron density topology data. Most metrics agree that the later An-Cl bonds are less ionic than might be anticipated on the basis of trends in the first half of the series, due to energy degeneracy-driven covalency in the β spin manifold; for example, the An-Cl QTAIM delocalisation index (bond order) for MdCl3 (0.88) is almost exactly the same as for NpCl3 (0.89). By contrast, the ratio of the kinetic to potential energy densities at the An-Cl bond critical points indicates that ionicity increases across the series, suggesting that the delocalisation index measures both orbital overlap and energy degeneracy-based covalency, while the bond critical point metric gauges only the former. Recalculation of all the data using the generalised gradient approximation PBE functional finds larger energy degeneracy-driven covalency in the later actinides than using hybrid DFT. Hence, we find that conclusions concerning the covalency of the An-Cl bond are dependent not only on the metric used to evaluate it, but also on the underlying electronic structure method.