Joint Crystal Structure and Computational Study of Hydrogen Bonds of Ethylenediamine

The hydrogen bonds of coordinated ethylenediamine (en) play important roles in catalytic activity [1], the aim of this work was to study geometrical parameters and strength of these interactions. The search of crystal structures archived in Cambridge Structural Database (CSD) was performed in order to find crystal structures containing at least one coordinated en to a transition metal, and at least one free water molecule interacting with en via NH···O hydrogen bond. All calculations were performed at M06L-GD3/def2-TZVPP/BSSE level of theory since it was confirmed that this level gives a good agreement with the CCSD(T)/CBS level. The distribution of dOH (Fig. 1) showed the maximum is at 2.0 Å - 2.1 Å, with a relatively large number of structures with distances shorter than 2.0 Å. The distribution of α (Fig 1.) revealed the maximum at 150⁰ - 160. The dOH and α are correlated, i.e. shorter distances correspond to larger angles. Most of en complexes contain cobalt, followed with palladium, nickel, and copper and most of them are in octahedral geometry. The coordination of en to the metal ions strengthens its hydrogen bonds with a water molecule. Namely, the energy of hydrogen bond of noncoordianted ethylenediamine is -2.3 kcal/mol, while the interaction energies for neutral metal complexes are in the range of -4.0 kcal/mol to -6.7 kcal/mol. Increasing of charge of complexes increases the energy of hydrogen bond. For singly charged complexes energy spans from -8.5 to -11.8 kcal/mol; for doubly charged complexes it spans from -15.6 kcal/mol to -19.9 kcal/mol; while triply charged complex has the strongest interaction of -28.0 kcal/mol [2]. In addition, the energies of hydrogen bond have a good correlation with the electrostatic potential on interacting hydrogen atom

Thermochemistry of organometallic reactions in solution: joint ITC and DFT study

The understanding of certain, still unknown, aspects of the chemical bond is made possible by new theoretical tools, particularly static DFT-D or DFT methods corrected for dispersion. These methods allow accounting for, in a physically relevant way, the effects of dispersion at medium and long distance [1]. For the further assessing the accuracy of static DFT-D calculations the providing of referential experimental data was found to be essential. It has been shown that Isothermal titration calorimetry (ITC) techniques can provide reliable thermodynamic parameters of reaction (enthalpy ΔHr, Gibbs free energy ΔGr and entropy ΔSr) [2], while some recent studies showed good agreement between experimental and theoretical results [2]. The study presented here sheds some light on the thermochemistry of reactions in solution by preforming ITC experiments in chlorobenzene and static DFT-D calculations. The study points out that, in cases where solvent molecules can interact significantly with molecules of reactants, an accounting for the explicit solvation is of crucial importance for agreement between experiment and theory. The results of various kinds of organometallic reactions will be presented in some details

The NH···O Interaction of Coordinated Ammonia and Ethylenediamine

The Cambridge Structural Database (CSD) search was used to find contacts of coordinated ammonia and coordinated ethylenediamine with water molecule.[1,2] The criteria for contacts were the dHO distance less than 4.0 Å and the angle α (N-H∙∙∙O) larger than 110°. The results from CSD search have shown that the peak of dHO distance for coordinated ammonia is in the 2.0 Å to 2.2 Å range, while the most abundant dHO distance for ethylenediamine is shorter, lying within the 1.8 Å to 2.0 Å range. The distribution of α angle for coordinated ammonia is without clear preference while for ethylenediamine tendency for more linear angle is pronounced. The interaction energy of free ammonia and of free ethylenediamine with water molecule are the same, -2.3 kcal/mol. The interaction energies for coordinated ammonia and coordinated ethylenediamine are significantly stronger. The interaction energies for singly and doubly charged ammonia complexes are -5.0 kcal/mol and -10.7 kcal/mol, respectively. The interaction energies for neutral, singly and doubly charged ethylenediamine are -6.7 kcal/mol, -11.8 kcal/mol and -19.9 kcal/mol, respectively. The interaction for ethylenediamine is stronger than for ammonia molecule due to somewhat stronger electrostatic interactions

Joint ITC and DFT Study of the Affinity of Some Lewis Bases to HIFP in Solution

HFIP, i.e. 1,1,1,3,3,3-hexafluoropropan-2-ol, was found to be an exceptional medium,[1] either as solvent or co-solvent, that allows many reactions to occur.[2-5] However, the exact role and mode of action of HFIP in various chemical transformations still remains elusive. Despite many reports dealing with water/HFIP complexes, little has been published on other molecular complexes of HFIP as well as on thermochemistry of the formation of such complexes.[6] Within this study the affinity of a series of eight different Lewis bases (3 sulfoxides, 3 Nsp2 pyridine derivatives, 1 aromatic amine, 1 cyclic aliphatic ether) to HFIP (as Lewis acid) is investigated experimentally by Isothermal Titration Calorimetry (ITC) and theoretically using static DFT-D calculations. Measured ITC association enthalpy values ΔHaITC spanned -9.3 kcal/mol - -14 kcal/mol. Computations including a PCM implicit solvation model produced similar exothermicity of association of all studied systems - ΔHa values ranging -8.5 – -12.7 kcal/mol. In general, most of interaction energy is due to the hydrogen bonding and not due to formation of significantly strong halogen bonds. An additional set of calculations combining implicit and explicit solvation by chlorobenzene of the reactants, pointed out the relatively low interference of the solvent with the HFIPbase complexation, which main effect is to slightly enhance the Gibbs energy of the HFIP-Lewis base association. It is speculated that the interactions of bulk HFIP with Lewis bases therefore may significantly intervene in catalytic processes not only via the dynamic miscrostructuration of the medium but also more explicitly by affecting bonds’ polarization at the Lewis bases

Can the Benzene-Benzene and Water-Water Interactions be Similar?

Benzene and water are quite different by nature, benzene molecule does not have a dipole moment, while water molecule does. Considering these properties of water and benzene molecules, one can expect very different benzene/benzene and water/water interactions. We have analyzed the benzene/benzene and water/water interactions found in crystal structures from CSD and we found that both benzene/benzene and water/water can form antiparallel interactions. Data from crystal structures in CSD shows that most benzene/benzene interactions are stacking interactions with large horizontal displacements, not the geometries that are minima on benzene/benzene potential surface. In these antiparallel interactions, the dipole moment of the C-H bond plays an important role. Also, in water/water interactions, there are a significant number of antiparallel interactions. Antiparallel interactions account for 20% of all attractive water/water contacts in the CSD. These antiparallel interactions result from the interaction of two O-H bonds in which dipoles are in antiparallel orientation. This shows that although these two molecules are very different, they can have similar interactions concerning the local dipole moment. The deciding factor for these two important interactions is antiparallel dipole moments of the O-H and C-H bond

The first Re(V) Complex with a Ligand from the Nature: Non-Covalent Interactions from Crystal Structure

A lot of scientific effort was dedicated to research into a cure for cancer over past decades. Many of them failed due to a low solubility of synthetized compounds or low selectivity between healthy and pathogenic cells. It was shown that apigenin, a natural pigment of chamomile, showed some cytotoxic activity itself,[1] however, its extremely low solubility in water is a limiting factor in its use as a potential anticancer drug. Here, we present a crystal structure of the first Re(V) complex containing apigenin – a natural occurring ligand. Various types of non-covalent interactions were found in the crystal structure (Figure 1). Namely, there are a couple of different hydrogen bonds (i.e. mono and bifurcated O-H∙∙∙O; O-H∙∙∙Cl; C-H∙∙∙Cl), T-shaped C-H∙∙∙π and π∙∙∙π stacking interactions. At least some of these interactions could be responsible for compounds’ final mechanism of anticancer action

Structure of water molecule and water hydrogen bonding: joint Cambridge Structural Database and ab-initio calculations study

In this study we performed analysis of non-coordinated water containing structures archived in Cambridge Structural Database (CSD), as well as ab-initio calculations on a range of bond lengths and bond angles of water molecule and water dimers

Theoretical and experimental evaluation of K2Br+ and K3Br+ clusters' ionization energies

In current study, a non-stoichiometric bromine-doped potassium K2Br+and K3Br+clusters are generated by combining a Knudsen effusion cell as a chemical reactor with thermal or surface ionization,and selected by a magnetic sector mass spectrometer. Furthermore, their ionization energies (IEs) are calculated for the first time using B3LYP/9-ve PP(K),cc-pVTZ-PP(Br) level of theory. Herein, presented results indicate that experimentally obtained IEs by Ionov equation, 4.10 ± 0.20 eV for K2Br+, and 4.03 ± 0.20 eV for K3Br+, are in consistence with their theoretically determined IEs.Physical chemistry 2016 : 13th international conference on fundamental and applied aspects of physical chemistry; Belgrade (Serbia); 26-30 September 2016

Regulation of nitric oxide production in hypothyroidism

Hypothyroidism is a common endocrine disorder that predominantly occurs in females. It is associated with an increased risk of cardiovascular diseases (CVD), but the molecular mechanism is not known. Disturbance in lipid metabolism, the regulation of oxidative stress, and inflammation characterize the progression of subclinical hypothyroidism. The initiation and progression of endothelial dysfunction also exhibit these changes, which is the initial step in developing CVD. Animal and human studies highlight the critical role of nitric oxide (NO) as a reliable biomarker for cardiovascular risk in subclinical and clinical hypothyroidism. In this review, we summarize the recent literature findings associated with NO production by the thyroid hormones in both physiological and pathophysiological conditions. We also discuss the levothyroxine treatment effect on serum NO levels in hypothyroid patients. © 2020 The Author

Antiparallel Noncovalent Interactions

In spite of being quite different substances, benzene and water can form similar noncovalent interactions. Analysis of the data in the crystal structures in the Cambridge Structural Database (CSD) revealed similarities in benzene/benzene and water/water interactions, since both benzene/benzene and water/water can form antiparallel interactions. The quantum chemical calculations of potential surface of water/water interactions showed that the minimum is hydrogen bond. Analysis of the data in the crystal structures in the Cambridge Structural Database (CSD) revealed antiparallel water/water interactions, in addition to classical hydrogen bonds (1). The geometries of all water/water contacts in the CSD were analyzed and for all contacts interaction energies were calculated at accurate CCSD(T)/CBS level. The results showed that the most frequent water/water contacts are hydrogen bonds; hydrogen bonds are 70% of all attractive water/water interactions. In addition, water/water contacts with antiparallel interactions are 20% of all attractive water/water contacts. In these contacts O-H bonds of water molecules are in antiparallel orientation (Figure). The quantum chemical calculations of potential surface of benzene/benzene interactions showed two minima stacking (parallel displaced) geometry and T-shaped geometry. Analysis of all benzene/benzene contacts in the crystal structures in the CSD revealed the most frequent benzene/benzene geometries (2). Majority of the benzene/benzene interactions in the CSD are stacking interactions with large horizontal displacements, and not geometries that are minima on benzene/benzene potential surface. In benzene/benzene interactions at large horizontal displacements two C-H bonds are in the antiparallel orientation (Figure). In these O-H and C-H antiparallel interactions two dipoles are in antiparallel orientation enabling close contact of positive and negative regions of the dipoles. Symmetry Adapted Perturbation Theory (SAPT) analysis showed that electrostatic is the largest attractive force in the antiparallel interactions. Antiparallel interactions are also possible between O-H and C-H bonds; in the crystal structures from the CSD these interactions are observed as one of the types of water benzene interactions (3)