Total Stabilization Energy Research Articles

The Persistence of Hydrogen Bonds in Pyrimidinones: From Solution to Crystal.

Pyrimidinone scaffolds are present in a wide array of molecules with synthetic and pharmacological utility. The inherent properties of these compounds may be attributed to intermolecular interactions analogous to the interactions that molecules tend to establish with active sites. Pyrimidinones and their fused derivatives have garnered significant interest due to their structural features, which resemble nitrogenous bases, the foundational building blocks of DNA and RNA. Similarly, pyrimidinones are predisposed to forming N-H···O hydrogen bonds akin to nitrogenous bases. Given this context, this study explored the supramolecular features and the predisposition to form hydrogen bonds in a series of 18 substituted 4-(trihalomethyl)-2(1H)-pyrimidinones. The formation of hydrogen bonds was observed in solution via nuclear magnetic resonance (NMR) spectroscopy experiments, and subsequently confirmed in the crystalline solid state. Hence, the 18 compounds were crystallized through crystallization assays by slow solvent evaporation, followed by single-crystal X-ray diffraction (SC-XRD). The supramolecular cluster demarcation was employed to evaluate all intermolecular interactions, and all crystalline structures exhibited robust hydrogen bonds, with an average energy of approximately -21.64 kcal mol-1 (∼19% of the total stabilization energy of the supramolecular clusters), irrespective of the substituents at positions 4, 5, or 6 of the pyrimidinone core. To elucidate the nature of these hydrogen bonds, an analysis based on the quantum theory of atoms in molecules (QTAIM) revealed that the predominant intermolecular interactions are N-H···O (average of -16.55 kcal mol-1) and C-H···O (average of -6.48 kcal mol-1). Through proposing crystallization mechanisms based on molecular stabilization energy data and contact areas between molecules and employing the supramolecular cluster and retrocrystallization concepts, it was determined that altering the halogen (F/Cl) at position 4 of the pyrimidinone nucleus modifies the crystallization mechanism pathway. Notably, the hydrogen bonds present in the initial proposed steps were confirmed by 1H NMR experiments using concentration-dependent techniques.

Atomic-resolution structure analysis inside an adaptable porous framework

We introduce a versatile metal-organic framework (MOF) for encapsulation and immobilization of various guests using highly ordered internal water network. The unique water-mediated entrapment mechanism is applied for structural elucidation of 14 bioactive compounds, including 3 natural product intermediates whose 3D structures are clarified. The single-crystal X-ray diffraction analysis reveals that incorporated guests are surrounded by hydrogen-bonded water networks inside the pores, which uniquely adapt to each molecule, providing clearly defined crystallographic sites. The calculations of host-solvent-guest structures show that the guests are primarily interacting with the MOF through weak dispersion forces. In contrast, the coordination and hydrogen bonds contribute less to the total stabilization energy, however, they provide highly directional point interactions, which help align the guests inside the pore.

A fully conjugated imidazole-fused perylene phenantroline ruthenium(II) complex in photocatalytic oxidation

In this investigation, the suitability of a specially designed imidazole-fused perylene ruthenium(II) molecule, denoted as Ru-PhP, was explored by employing the photooxidation of 1,5-dihydroxynaphthalene (DHN) to produce Juglone as a model reaction. This distinctive, entirely conjugated compound was synthesized through the reaction between perylene imide anhydride dye (1) and a ruthenium(II) phenanthroline complex (2) in the presence of a Zn(OAc)2 catalyst. Structural analyses of the compound were performed by using general spectroscopic methods including FT-IR, 1H NMR, 13C- NMR, and MALDI-TOF analyses. Various photophysical properties, including the UV–Vis absorption spectrum, fluorescence emission spectrum, and fluorescence quantum yield, were examined. The photochemical studies via indirect method endorsed Ru-PhP as an efficient photosensitizer. Furthermore, Ru-PhP proved to be highly effective in facilitating the photooxidation of DHN to yield juglone. DFT-based natural bond orbital analysis revealed intramolecular charge transfer in Ru(II) coordination environment, with a strong total stabilization energy (25.31 eV) between the ruthenium acceptor and nitrogen donors in the bipyridine and phenanthroline units. The dispersion of HOMO electrons within the imidazole-bridged perylene moiety and the localization of LUMO electrons near Ru(II)-coordinated bipyridine units were observed through Frontier Molecular Orbital and molecular electrostatic potential analyses. Ru-PhP is proposed as photocatalyst for photo redox catalytic organic reactions.

Molecular structure, spectroscopy, molecular docking, and molecular dynamic studies of tetrahydroneoprzewaquinone as potent cervical cancer agent

Abstract Cervical cancer is one of the most prevalent cancer-related diseases, causing accelerated morbidity and mortality rates in low-income countries and African states. This study explores the potential of (3R,3′R)-2,2′,3,3′-tetrahydroneoprzewaquinone (TDN) as a treatment for cervical cancer by investigating its structural and molecular properties using molecular modelling technique, which include; DFT, molecular docking, molecular dynamic simulation. The results are promising, with TDN demonstrating exceptional stability in the energy gap (E g) as well as through natural bond order analysis (NBO). π → σ* electronic transitions were found to contribute mainly to the molecule’s stability, with an outstanding total stabilization energy (E (2)). Docking exercises showed that TDN binds more favorably to the pro-apoptotic receptor 4s0o with a stronger H-bond compared to the conventional DOX drug, which interacted less effectively with TDN and more strongly with the anti-apoptotic protein, forming an outstanding strong H-bond. Molecular dynamics simulations also revealed that TDNʼs interaction with the pro-apoptotic protein (TDN_4S0o) was more stable than the standard DOX drug (DOX_4s0o). The H-bond plot indicated that TDN could effectively interact with both anti and pro-apoptotic receptors, forming approximately 1 to 4 hydrogen bonds between TDN_1g5M with respect to each picosecond (ps) ranging from 0 to 1000 ps. In contrast, the number of hydrogen bonds fluctuated when DOX interacted with the anti-apoptotic protein (1g5M), ranging from 1 to 5 H-bonds. Overall, these results suggest that TDN may be a promising drug candidate for cervical cancer treatment.

Nature and strength of metal-dichalcogenolate bond in homoleptic square-planar d8 metal bis(1,2-dichalcogenolate) complexes [M(E2C2(CN)2)2]2– (E=S, Se, Te; M=Ni(II), Pd(II), Pt(II)): A DFT study

In this work, the interactions between the fragments in homoleptic square-planar d8 metal bis(1,2-dichalcogenolate) complexes [M(E2C2(CN)2)2]2– (E = S, Se, Te; M=Ni(II), Pd(II), Pt(II)) have been investigated by using density functional theory (BP86, M06) calculations with a focus on the nature of metal−dichalcogenolate bonds. Four types of interaction energies between the fragments, the deformation energies of metal and dichalcogenolate ions as well as the total interaction and stabilization energies of the complexes were calculated and compared. An energy decomposition analysis (EDA) was also performed to study the nature of metal−bis(dichalcogenolate) bonds in these complexes. The results showed that the stabilization and total interaction energies are decreased by changing the chalcogen atom from sulfur to selenium and from selenium to tellurium ([M(S2C2(CN)2)2]2– > [M(Se2C2(CN)2)2]2– > [M(Te2C2(CN)2)2]2–). The analysis of metal−bis(dichalcogenolate) bonds showed that the orbital interactions are mainly Metal←Lσ and have considerably less contribution to the total attractive interactions compared to electrostatic interactions. However, the contribution of orbital interactions, in an opposite trend with the interaction energies, is increased by changing the chalcogen atom from sulfur to selenium and from selenium to tellurium.

Non-covalent interactions towards 2-(4-(2,2-dicyanovinyl) benzylidene)malononitrile packing polymorphism due to solvent effect. Experimental and theoretical spectroscopy approach

Two polymorphs of 2-(4-(2,2-dicyanovinyl)benzylidene)malononitrile (I) were obtained by slow evaporation in acetone (Ia) and acetonitrile (Ib). These two polymorphic forms were analyzed by single-crystal XRD, which revealed both crystallized in the monoclinic crystal system and space group P21/n with Z = 2 (Z′= 0.5). Also, the SCXRD analysis evidenced that in the solvent-induced packing polymorphism; the Ia compound molecules are arranged in a slipped stacking pattern formed through the π···π interactions; while Ib molecules are arranged in a herringbone pattern stabilized by the intermolecular CH···N interactions. Packing polymorphism affects the fluorescence; for Ia crystals, the maximum emission wavelength was at 500 nm and for Ib was at 482 nm. The molecule structure features two C–C bonds with free rotation allowing conformational variation between polymorphs, and the principal difference is in molecular packing due to intramolecular and intermolecular interactions. The intermolecular interaction energies for the molecular dimers were obtained by the PIXEL method. The total lattice energy estimated using PIXELC module, was 32.71 and 34.03 kcalmol−1, for Ia and Ib, respectively; Ib showed a lower contribution of %Edis towards the total stabilization energy and might be due to a more significant number of stacking interactions formed in the crystal packing. Hirshfeld surface (HS) analysis and 2D-fingerprint plots were used to evaluate the relative contribution of non-covalent interactions (NCI) towards the crystal packing. The topology parameters suggested that the intermolecular interactions are weaker, and purely van der Waals and NCI plots were used to visualize the nature of non-covalent interactions. The complete assignments of all vibrational modes computed with potential energy distributions (PEDs) using the VEDA were in good agreement with experimental values; the difference is for the CN-stretching bands caused for the intramolecular interactions indicating possible charge transfer (CT). Natural bond orbital (NBO) analysis and electrostatic potential surfaces (MEPS) were performed to estimate the donor and acceptor sites in the molecule. Additionally, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and absorption wavelength were calculated by the time-dependent DFT approach. Using 1H and 13C chemical shifts to determine interactions before crystallization. The physicochemical characterization for both Ia and Ib did not show important differences using analytical techniques FT-IR, NMR, DSC/TGA, and PXRD.

Stabilization of Interstellar CSi2 Species by Donor Base Ligands: L-CSi2-L; L = cAACMe, NHCMe, and PMe3.

The donor ligand bonded singlet (L)2Si2C containing a bent Si2C unit in the middle has been studied by theoretical quantum mechanical calculations (NBO, QTAIM, EDA-NOCV analyses) [L = cAAC, NHC, Me3P]. EDA-NOCV analysis suggests that this Si2C is possible to stabilize by a pair of donor base ligands. The bond dissociation energy of the Si2C fragment is endothermic (85-45 kcal/mol) with a sufficiently high intrinsic interaction energy (ΔEint = -89 to -48 kcal/mol). Fifty percent of the total stabilization energy arises from electrostatic interactions, and nearly 45% is contributed by covalent orbital interaction between Si2C and (L)2 fragments in their singlet states. 75-80% of the orbital interaction energy is contributed by two sets of σ-donation L → SiCSi ← L. The π-back-donation is only 15-10%. The dispersion energy is not negligible (3-5%). The interaction energy is highest for 1 (L = cAAC) among three compounds. Additionally, (cAAC)2Si2C-Ni(CO)3 (4) has been studied. The interaction energy between 1 and Ni(CO)3 is nearly 61 kcal/mol with the major contribution coming from donation of electron cloud from electron rich Si2C backbone to empty hybrid orbital of Ni(CO)3 fragment. A sufficiently strong π-back-donation from (OC)3Ni to Si2C has also been identified.

New rhodium(III)-ED3AP complex: Crystal structure, characterization and computational chemistry

Only one (trans(O5)-Na[Rh(ED3AP)]?3H2O) of possible two isomers was synthesized and characterized by single crystal X-ray analysis, IR and UV?Vis spectroscopy. Computational analysis of both isomers was performed with three levels of theory (B3LYP/TZV, BP86/TZV, OPBE/TZV), which gave consistent results. The more stable isomer by total energy and ligand field stabilization energy (LFSE) was trans(O5) which appeared in synthesis. The calculation of excited state energies complied with UV?Vis spectra, especially with OPBE functional. The results of excited state energy pointed out the differences among isomers in means of a splitting pattern of 1T2g excited state term. Both isomers have a strongly delocalized structure, according to the natural bonding orbital (NBO) analysis. NBO analysis shows that the trans(O5) isomer is more stable than trans(O5O6) for approx. 87 kJ/mol. Therefore, only the trans(O5) isomer is present in the reaction mixture.

On the Many-Body Expansion of an Interaction Energy of Some Supramolecular Halogen-Containing Capsules.

A tetramer model was investigated of a remarkably stable iodine-containing supramolecular capsule that was most recently characterized by other authors, who described emergent features of the capsule’s formation. In an attempt to address the surprising fact that no strong pair-wise interactions between any of the respective components were experimentally detected in condensed phases, the DFT (density-functional theory) computational model was used to decompose the total stabilization energy as a sum of two-, three- and four-body contributions. This model considers complexes formed between either iodine or bromine and the crucial D4d-symmetric form of octaaryl macrocyclic compound cyclo[8](1,3-(4,6-dimethyl)benzene that is surrounded by arenes of a suitable size, namely, either corannulene or coronene. A significant enthalpic gain associated with the formation of investigated tetramers was revealed. Furthermore, it is shown that the total stabilization of these complexes is dominated by binary interactions. Based on these findings, comments are made regarding the experimentally observed behavior of related multicomponent mixtures.

Crystal structures, Hirshfeld surface analysis and PIXEL calculations of two chalcone derivatives, containing isopropoxy substituents: Importance of dispersion energy

The crystal structures, Hirshfeld surface analysis and PIXEL calculations are reported for (E)-3-(4-methoxyphenyl)-1-(2-hydroxy-5-isoproproxyphenyl)prop-2-en-1-one, 1, and (E)-3-(3-methoxy-4-isopropoxyphenyl)-1-(2-hydroxy-4,6-diisoproproxyphenyl)prop-2-en-1-one, 2. Different sets of C—H···O, C—H···π, off-set, face-to-face π ···π and/or C=O··· π intermolecular interactions are displayed by each compound. Due to the bulk of the isoproproxy unit and the consequent steric hindrance in forming aggregates in the solid state, compounds 1 and 2 exhibit larger interplanar angles than do corresponding chalcones with methoxy units. The total stabilization energies of the crystal packing, Etot distributed as Coulombic (Ecoul), polarization (Epol), dispersion (Edisp), and repulsion (Erep) have been computed by PIXEL. For compound 1, six motifs (molecule pairs) and for compound 2, with two independent molecules in the asymmetric unit, thirteen motifs are identified by the PIXEL calculations to have energies, -Etot, above the cut-off value of 10 kJ.mol−1. For each of these motifs, the largest contributor to the Etot value is the Edisp term, irrespective of the type(s) of interaction(s) connecting the two molecules, if any, in the motifs.

Formation of a penta- or hexacoordinated Cu−(II) semicarbazone complex: Revisiting semicarbazone metal complexes

The structural characterization of a new pentacoordinated semicarbazone copper complex, [Cu(N,N',O-HSCPy)(N,N'-HSCPy)][ClO4]2 (1) is reported. The structure of 1 was compared to the hexacoordinated complex, [Cu(N,N',O-HSCPy)2][ClO4]2⋅H2O (2), which was already published, to shed some light on the formation of both forms. Energetic data of Cu-ligand bonds showed that the absence of a Cu-O bond in cation 1 does not significantly change the total stabilization energy in the pentacoordinate cation relative to the hexacoordinate cation (less than 4%). This is because the Cu-ligand bonds have their energies redistributed into the five existing bonds of 1. Additionally, we extended the study revisiting analogous HSCPy complexes with other coordinated metals (M), with general formula [M(N,N',O-HSCPy)2][X]2⋅solvent, where M = Ni (3), Co (4), Zn (5), Fe (6), and Mn (7); X = ClO4, and solvent = H2O (3-6) or EtOH (7); and complex [Cu(N,N',O-HSCPy)2][ClO4][I3] (8) was included in this series. In general, all additional complexes showed similar behavior to that of the Cu-hexacoordinated complex (2). In this sense, was possible to observe that the energies of the bonds M-O and M-N have strong linear correlation in the three groups: M-O3′//M-O3, M-N1′//M-N1, and M-N2′//M-N2, for complexes 2-7 (r = 0.9766; N = 18). Also, a strong correlation between stabilization energy data of metal-ligand and their respective bond lengths (r =0.9393; N = 47) was observed in all studied complexes (1-8). The supramolecular geometric similarity index ID was calculated comparing 2 with 1, 3-8. It was observed a high geometric similarity between 2 and 3-6 (ID < 0.95), indicating an isostructural behavior. The comparison between 2 and complexes 1,8 indicated values in the intermediate region (ID = 0.75) and close to a border region with an intermediate-to-high region of similarity (ID = 0.83), respectively. The similarity comparison between 2 and 7 had a value of 0.77, in the intermediate region of similarity, showing that the change of a water molecule for an ethanol molecule considerably affected the crystal packing.

Crystal structure, Hirshfeld surface analysis and PIXEL calculations of the three isomeric (E)-2-((pyridinylmethylidene)hydrazinyl)benzo[d]thiazoles: Occurrence of stacking interactions

Detailed structural analyses, utilizing crystal structure determinations, Hirshfeld surface analysis and PIXEL calculations have been carried out on the three isomeric (E)-2-((pyridin-X-ylmethylidene)hydrazinyl)-benzo[d]thiazoles: [1: 2-py] (X = 2), [1: 3-py] (X = 3), and [1: 4-py] (X = 4). All compounds are near planar with the largest deviation from planarity experienced by the pyridin-2-yl derivative. The bond lengths in the linker units between the terminal aromatic groups indicate a degree of electionic delocalisation is occurring, which thus points to an extended π system being present for each complete molecule. Hirshfeld surface analysis and the PLATON analysis provided information on the close contacts and intermolecular interactions. Each compound has its own set of intermolecular hydrogen bonds and stacking interactions. The total stabilization energies of the crystal packing, Etot, distributed as Coulombic (Ecoul,), polarization (Epol), dispersion (Edisp) and repulsion (Erep) components, are calculated by PIXEL. The energy contributions (kJ.mol−1) for each molecule, in the order, Edisp, Ecoul, Epol and Erep, are for compound [1: 2-py] -86.2, -43.8, -180.8 and 165.3 kJmol−1, for compound [1: 3-py] -98.4, -50.1, -188.4, 187.8 kJ.mol−1, and for compound [1: 4-py] – 88.9, -40.8, -194.9 and 164.5 kJ.mol−1 respectively. For [1: 2-py], [1: 3-py] and [1: 4-py], the number of motifs (molecule pairs) indicated by PIXEL to have energies above the cut-off value of -10 kJ.mol−are six, seven and seven, respectively. While the most energetically favourable motif in each compound is formed from N—H···N hydrogen bonds, with the ECoul term being the biggest contributor to Etot., different intermolecular hydrogen bonds are involved: the hydrogen bonds in [1: 2-py] and [1: 4-py], involve hydrazonyl moieties, ie. N—H(hydrazonyl)···N(hydrazonyl) with formation of R22(8) dimers, and in compound, [1: 3-py], C(7) chains are formed from N—H(hydrazonyl) ···N(pyridinyl) hydrogen bonds. The remaining motifs for all three compounds have Edisp as the biggest contributor to their stabilities. The percentage atom··· atom contacts were obtained from partial analysis of the PIXEL calculations: for both compounds [1: 2-py], [1: 3-py] and [1: 4-py], the three highest percentage atom···atom contacts were H···H (ca. 37%), H···C / C···H (ca.23%) and H···N/ N···H (ca. 17)%.

How the oxazole fragment influences the conformation of the tetraoxazocane ring in a cyclohexanespiro-3'-(1,2,4,5,7-tetraoxazocane): single-crystal X-ray and theoretical study.

Single crystals of (2S,5R)-2-isopropyl-5-methyl-7-(5-methylisoxazol-3-yl)cyclohexanespiro-3'-(1,2,4,5,7-tetraoxazocane), C16H26N2O5, have been studied via X-ray diffraction. The tetraoxazocane ring adopts a boat-chair conformation in the crystalline state, which is due to intramolecular interactions. Conformational analysis of the tetraoxazocane fragment performed at the B3LYP/6-31G(d,2p) level of theory showed that there are three minima on the potential energy surface, one of which corresponds to the conformation realized in the solid state, but not to a global minimum. Analysis of the geometry and the topological parameters of the electron density at the (3,-1) bond critical points (BCPs), and the charge transfer in the tetraoxazocane ring indicated that there are stereoelectronic effects in the O-C-O and N-C-O fragments. There is a two-cross hyperconjugation in the N-C-O fragment between the lone electron pair of the N atom (lpN) and the antibonding orbital of a C-O bond (σ*C-O) and vice versa between lpO and σ*C-N. The oxazole substituent has a considerable effect on the geometry and the topological parameters of the electron density at the (3,-1) BCPs of the tetraoxazocane ring. The crystal structure is stabilized via intermolecular C-H...N and C-H...O hydrogen bonds, which is unambiguously confirmed with PIXEL calculations, a quantum theory of atoms in molecules (QTAIM) topological analysis of the electron density at the (3,-1) BCPs and a Hirshfeld analysis of the electrostatic potential. The molecules form zigzag chains in the crystal due to intermolecular C-H...N interactions being electrostatic in origin. The molecules are further stacked due to C-H...O hydrogen bonds. The dispersion component in the total stabilization energy of the crystal lattice is 68.09%.

2]Rotaxanes Bearing a Tetralactam Macrocycle: The Role of a Trifurcated Hydrogen Bond in the Crystalline State

This study investigated the proper classification and quantification of intercomponent trifurcated hydrogen bonds, in the crystalline state, of rotaxanes bearing a tetralactam Leigh‐type macrocycle. Quantum mechanical calculations were carried out to obtain the interaction paths and their stabilization energies. In general, the use and necessity of fragmentation in types of interaction have been reported in the literature, although they are commonly performed only using a geometric approach. This results in N–H···O interactions that are indicated as the main interactions between components, neglecting other possible interactions. The use of energetic fragmentation was demonstrated here under an appropriate demarcation considering all interactions and showing the existence and role of the C–H···O interaction. The C–H···O interactions showed similar energy to N–H···O interactions with average values around –4.75 kcal mol–1and –4.60 kcal mol–1, respectively. This revealed that the three hydrogen bonds are part of a cooperative set of interactions with a similar contribution. The trifurcated hydrogen bonds presented high contribution in the total intercomponent stabilization energy of the rotaxanes, with an average value of 51 % in the studied series.

Remarkable shifts of Csp2 -H and O-H stretching frequencies and stability of complexes of formic acid with formaldehydes and thioformaldehydes.

Thirty-six stable complexes of formic acid with formaldehydes and thioformaldehydes were determined on the potential energy surface, in which the XCHO···HCOOH complexes are found to be more stable than the XCHS···HCOOH counterparts, with X = H, F, Cl, Br, CH3 , NH2 . All complexes are stabilized by hydrogen bonds, and their contribution to the total stabilization energy of the complexes increases in going from C-H···S to C-H···O to O-H···S and finally to O-H···O. Remarkably, a significant blueshift of Csp2 -H bond by 81-96 cm-1 in the Csp2 -H···O hydrogen bond has hardly ever been reported, and a considerable redshift of O-H stretching frequency by 206-544 cm-1 in the O-H···O/S hydrogen bonds is also predicted. The obtained results in our present work and previous literatures support that a distance contraction and a stretching frequency blueshift of C-H bond involving hydrogen bond depend mainly on its polarity and gas phase basicity of proton acceptor, besides the rearrangement of electron density due to complex formation. Markedly, we suggest the ratio of deprotonation enthalpy to proton affinity (R c ) as an indicator to prospect for classification of hydrogen bonds. The symmetry adapted perturbation theory results show a larger role of attractive electrostatic term in XO-n as compared to that in XS-n and the electrostatic interaction is overwhelming dispersion or induction counterparts in stabilizing XO-n and XS-n, with n = 1, 2, 3. © 2019 Wiley Periodicals, Inc.

Nature and Hierarchy of Hydrogen-Bonding Interactions in Binary Complexes of Azoles with Water and Hydrogen Peroxide.

In the present study, the hydrogen-bonded complexes of azole with water and hydrogen peroxide are systematically investigated by second-order Møller–Plesset perturbation theory and density functional theory with dispersion function calculations. This study suggests that the ability of pyrrolic nitrogen (NH) atom to function as hydrogen-bond donor increases with the introduction of nitrogen atoms in the ring, whereas the ability of pyridinic nitrogen (N) atom to act as hydrogen-bond acceptor reduces with successive aza substitution in the ring. With introduction of nitrogen atoms in the ring, the vibrational frequency, stabilization energy, and electron density in the σ antibonding orbitals of the X–H (X = N, C of azole) bond of the complexes all increase or decrease systematically. Decomposition analysis of total stabilization energy showed that the electrostatic energy term is a dominant attractive contribution in comparison to induction and dispersion terms in all of the complexes under study.

Binding, and thermodynamics of β-cyclodextrin inclusion complexes with some coumarin laser dyes and coumarin-based enzyme substrates: a simulation study

This paper addresses modelling the nature of interactions between β-CD and some coumarins including recently reported novel sulphur analogues to form inclusion complexes of appealing medicinal, photochemical and photophysical properties. The binding energy and the total stabilization energy (EONIOM) are used to confirm the most favorable inclusion complex structure. Thermodynamic parameters reveal exothermic inclusion reaction in gas phase. Thermal stability of fluorescent enzyme substrate of coumarin nucleus increases in the order: gas < cyclohexane < water, indicating better stability in water. Furthermore, molecular characteristics such as optimized geometries, MO’s and electrostatic potential energy map surfaces and energies are reported and correlated with some reactivity indices. Our results validated the experimentally available data reported in the literature. Inclusion complexes of β-CD with coumarins should result in improving its laser efficiency in environmentally benign aqueous medium.

Interaction of polyelectrolyte complex between sodium alginate and chitosan dimers with a single glyphosate molecule: A DFT and NBO study

The formation of a polyelectrolyte complex through dimers of alginate and chitosan in the presence of sodium cations (SA/CS), and its interaction with the glyphosate herbicide, has been investigated at the DFT level (B3LYP/6‒311+G(d,p)). The lowest energy structure for SA/CS presents one Na+ cation coordinated to both dimers and formation of two H-bonds involving COO– and NH3+. The coordination energy of Na+ contributes with about 40% of the total complex stabilization energy. LMOEDA method indicates important contribution of covalent nature to stabilization of SA/CS. This result is corroborated by NBO analysis which shows high contribution of lp(O)→σ*(NH) overlapping, with average energy of 30 kcal mol−1 for the formed H-bonds. Two water molecules neighboring the complex increases its stability and promotes an octahedral coordination arrangement around Na+. The glyphosate interacts with SA/CS coordinating to Na+ and bonding to the chitosan dimer by H–bond, in agreement to performed fluorescence microscopy measurements.

The Hydrogen bonding effects in structural analysis of phenilon C-2: the quantum-chemical interpretation

Using ab initio methods of quantum chemistry the structure and spectral properties for molecular complexes, which were formed by monomer of phenilon С-2 chain, including some intra- and intermolecular hydrogen bonding effects as well as electrostatic interactions with evaluation of their contributions in total stabilization energy, have been investigated at natural bond orbitals theory. It is shown, that the overlapping of n1,2(O)→ σ*(NН) type with energies 15.4 and 9.5 kJ/mol, which correspond to the strong hydrogen bonding between amide groups, is a main direction for co-operating of some area for structural fragments of macromolecules. The proposed theoretical models are validated in reflection of spectral and energetic parameters for investigating system.

Ammonia Borane Clusters: Energetics of Dihydrogen Bonding, Cooperativity, and the Role of Electrostatics.

Cluster formation of ammonia borane (NH3BH3) driven by noncovalent H···H dihydrogen interaction is investigated at the M06L/6-311+G(d,p) level of density functional theory. For clusters containing up to six monomers, ladder, cyclic, stacked, cross-stacked, end-on, mixed and hexagonal configurations have been screened for their energetic stability. In the dimer, 7.94 kcal/mol stabilization energy per monomer (Em) is observed. Compared to ladder and cyclic configurations, a tetramer consisting of stacked dimer units is more stable by 3.0 kcal/mol whereas a hexamer composed of hexagonally arranged monomers promoting side-on H···H interaction is more stable than a stacked configuration by 2.5 kcal/mol. The hexagonal packing of cluster is repeated to obtain (NH3BH3)12, (NH3BH3)18, (NH3BH3)36, (NH3BH3)48, and (NH3BH3)54 clusters. The Em 17.81 kcal/mol observed for (NH3BH3)54 is 2.24 fold higher than the dimer, suggesting strong cooperativity in cluster growth mechanism. The zwitterionic features of NH3BH3 is characterized in terms of molecular electrostatic potential (MESP) features. During cluster formation, donation of electron density from negatively charged BH3 unit of a monomer to the positively charged NH3 unit of other interacting monomers occurs through H···H dihydrogen bonding. The extent of electron donation is revealed through the value of MESP minium (Vmin) in every monomer. A strong linear correlation between the total value of Vmin for a cluster (ΣVmin) and the total stabilization energy of the cluster (Estb) is established. Further, MESP at the nuclei of N (VN) and B (VB) are found to be very sensitive to the strength of H···H bonding. With respect to free NH3BH3, the total change in VN (ΣΔVN) as well as the total change in VB (ΣΔVB) in a cluster shows near-perfect linear correlation with Estb. Further, the magnitude of the three quantities, viz. ΣΔVN, ΣΔVB, and Estb is nearly same and indicates that the cluster formation of NH3BH3 is almost effectively controlled by electrostatics of dihydrogen interactions. The extended network of dihydrogen interactions observed in large clusters and the significant positive cooperativity effect of such interactions support the use of ammonia borane as a potential hydrogen storage material.