Theoretical investigation on the structural and electronic properties of complexes formed by thymine and 2′-deoxythymidine with different anions

Hydrogen bonding interactions between thymine nucleobase and 2′-deoxythymidine nucleoside (dT) with some biological anions such as F⁻ (fluoride), Cl⁻ (chloride), OH⁻ (hydroxide), and NO₃ ⁻ (nitrate) have been explored theoretically. In this study, complexes have been studied by density functional theory (B3LYP method and 6-311++G (d,p) basis set). The relevant geometries, energies, and characteristics of hydrogen bonds (H-bonds) have been systematically investigated. There is a correlation between interaction energy and proton affinity for complexes of thymine nucleobase. The nature of all the interactions has been analyzed by means of the natural bonding orbital (NBO) and quantum theory atoms in molecules (QTAIM) approaches. Donors, acceptors, and orbital interaction energies were also calculated for the hydrogen bonds. Excellent correlations between structural parameter (δR) and electron density topological parameter (ρ _b) as well as between E(2) and ρ _b have been found. It is interesting that hydrogen bonds with anions can affect the geometry of thymine and 2′-deoxythymidine molecules. For example, these interactions can change the bond lengths in thymine nucleobase, the orientation of base unit with respect to sugar ring, the furanose ring puckering, and the C1′–N1 glycosidic linkage in dT nucleoside. Thus, it is necessary to obtain a fundamental understanding of chemical behavior of nucleobases and nucleosides in presence of anions.     

Theoretical study of N–H· · ·O hydrogen bonding properties and cooperativity effects in linear acetamide clusters

We investigated geometry, energy, ${\nu_{{\text{N--H}}}}$ harmonic frequencies, ¹⁴N nuclear quadrupole coupling tensors, and ${n_{\rm O}\to \sigma _{{\text{N--H}}}^\ast}$ charge transfer properties of (acetamide) _n clusters, with n = 1 ? 7, by means of second-order Møller-Plesset perturbation theory (MP2) and DFT method. Dependency of dimer stabilization energies and equilibrium geometries on various levels of theory was examined. B3LYP/6-311++G** calculations revealed that for acetamide clusters, the average hydrogen-bonding energy per monomer increases from ?26.85 kJ mol^?1 in dimer to ?35.12 kJ mol^?1 in heptamer; i.e., 31% cooperativity enhancement. The n-dependent trend of ${\nu_{{\text{N--H}}}\,{and}\,^{14}}$ N nuclear quadrupole coupling values were reasonably correlated with cooperative effects in ${r_{{\text{N--H}}}}$ bond distance. It was also found that intermolecular ${n_{\rm O}\to \sigma_{{\text{N--H}}}^\ast}$ charge transfer plays a key role in cooperative changes of geometry, binding energy, ${\nu_{{\text{N--H}}}}$ harmonic frequencies, and ¹⁴N electric field gradient tensors of acetamide clusters. There is a good linear correlation between ¹⁴N quadrupole coupling constants, C _Q (¹⁴N), and the strength of Fock matrix elements (F _ij ). Regarding the ${n_{\rm O}\to \sigma_{{\text{N--H}}}^\ast}$ interaction, the capability of the acetamide clusters for electron localization, at the N–H· · ·O bond critical point, depends on the cluster size and thereby leads to cooperative changes in the N–H· · ·O length and strength, N–H stretching frequencies, and ¹⁴N quadrupole coupling tensors.     

Theoretical studies on electronic structures and spectroscopic properties of a series of novel β-diketonate Os(II) complexes

The geometries, electronic structures, and spectroscopic properties of a series of [Os^(II)(CO)₃(tfa)(acac(X)₂)] (tfa = trifluoroacetate; acac = acetoylacetonate; X = H (1), CF₃ (2), C₆H₅ (3), and C₁₀H₇ (4)) complexes have been investigated theoretically. The ground and excited state geometries were optimized at the B3LYP/LANL2DZ and CIS/LANL2DZ levels, respectively. The optimized geometry structural parameters agreed well with the corresponding experimental results. As indicated in this paper, the highest occupied molecular orbitals were dominantly localized on the Os atom, ctfa (abbv. of CO and tfa), and acac ligand for 1 and 2, acac ligand and X substituent for 3 and 4, while the lowest unoccupied molecular orbitals were mainly composed of acac ligand and X substituent. Under the time-dependent density functional theory (TDDFT) level with the polarized continuum model (PCM), the absorption and phosphorescence in CH₂Cl₂ media were calculated based on the optimized ground- and excited-state geometries, respectively. The calculated results show that the lowest energy absorptions at 317 (1), 342 (2), 377 (3), and 420 nm (4) are attributed to a change of ππ*/MLCT mixing transition to pure ππ* transition for 1–4, while their phosphorescence emission have similar transition properties. This indicates that the absorption and emission transition characters could be altered by adjusting the π electron-donating ability.     

Characteristics of X-H···π interactions: ab initio and QTAIM studies

The MP2/6-311++G(d,p) calculations were performed on several hydrogen-bonded systems. Different complexes were taken into account to analyze various types of hydrogen bonds, possessing different types of proton donors and proton acceptors as well as characterized by the broad range of the interaction energy. The Quantum Theory of Atoms in Molecules is applied. The results of the hybrid variational-perturbational approach are discussed. The unique properties of hydrogen bonds, where π-electrons act as the proton acceptor (X-H···π), are analyzed, and these interactions are compared with the other types of hydrogen bonds, mainly with C-H···Y interactions. It is shown that for X-H···π systems the ellipticity at the bond critical point of the proton···acceptor interaction is much greater than for the other types of hydrogen bonds. However, both X-H···π and C-H···Y interactions are characterized by the dominance of the dispersive energy.     

Density functional theory and topological analysis on the hydrogen bonding interactions in N-protonated adrenaline–DMSO complexes

In this study, complexes formed via hydrogen bond interactions between N-protonated adrenaline (AdH⁺) and DMSO have been studied by density functional theory (DFT). The relevant geometries, energies, and IR characteristics of the hydrogen bonds (H-bonds) have been systematically investigated. The natural bond orbital (NBO) and the quantum theory of atoms in molecule (QTAIM) analysis have also been applied to understand the nature of the hydrogen bonding interactions in complexes. The H-bonds involving amino or hydroxyls as H-donor are dominant H-bonds in complexes and are attributed to strong H-bonds. The weak H-bonds, such as π H-bonds and H-bonds involving methyl (DMSO) or methenyls (C2H6 and C5H7 of AdH⁺) as H-acceptors, were found in complexes as well. The complexes in which the dominant H-bond involves amino of AdH⁺ as H-donor are more stable than those with the dominant H-bond involving hydroxyls as H-donor. Some relationships between various properties of QTAIM, NBO, geometry as well as frequency were also investigated.     

SH···N and SH···P blue-shifting H-bonds and N···P interactions in complexes pairing HSN with amines and phosphines

Quantum calculations at the MP2/aug-cc-pVDZ level examine complexes pairing HSN with aliphatic amines and phosphines. Complexes are cyclic and contain two attractive interactions. The first is a SH···N/P H-bond in which the S-H covalent bond contracts and shifts its stretching frequency to the blue, more so for amines than for phosphines. The second interaction is different for the amines and phosphines. The amines engage in a NH···N H-bond comparable in strength to the aforementioned SH···N interaction. In contrast, the second interaction in the phosphine complexes is a direct N···P attraction without an intervening H. This interaction is due in part to opposite partial charges on the N and P atoms, as well as covalent forces generated by charge transfer effects.     

Strong π-delocalization and substitution effect on electronic properties of dithienylpyrrole-containing bipyridine ligands and corresponding ruthenium complexes

The first dithienylpyrrole (DTP)-based bipyridine ligands has been prepared and coordinated with ruthenium to give the corresponding homoleptic complexes. Bipyridine was bound at pyrrole (DTP(1)) or thiophene (DTP(2)) ring. A strong bathochromic effect was obtained by switching from pyrrole to thiophene for ligands and complexes. Interestingly the DTP(2) series offered a wide absorption window from UV to visible domain with an almost constant absorbance. These effects are due to a larger extent of delocalization as supported by DFT calculations and photophysical measurements.     

Quantum chemical investigation on the structural and electronic properties of α-, β-, and γ-cyclodextrin complexes: DFT and QTAIM analysis

To characterize the structural, thermochemical and electronic aspects in complexes of leucine, vanillin and mechlorethamine with α-, β-, and γ-cyclodextrins (CDs), a density functional theory (DFT) study has been conducted in combination with quantum theory of atoms in molecules (QTAIM) analysis. The QTAIM method has been utilized to explore the nature of various possible interactions between leucine, vanillin and mechlorethamine with CDs in terms of bond critical points (BCPs). HOMO and LUMO and atomic charges studies show charge transfer occurs between drugs and cyclodextrins. This behavior has been also investigated via QTAIM charge analysis. On the other hand, based on QTAIM electronic energy indicators we have discussed electrostatic character of interactions between vanillin, leucine and mechlorethamine with inner surface CDs in the coordination sphere.     

Study on molecular and electronic structures, and spectroscopic properties of azide ruthenium complexes with pyridine and β-picoline ligands

The [Ru(N₃)₂(PPh₃)(py)₃] and [Ru(N₃)₂(PPh₃)₂(β-pic)₂] complexes have been prepared and studied by IR, NMR, UV-Vis spectroscopy and X-ray crystallography. The complexes were prepared in the reactions of [RuCl₂(PPh₃)₃] with pyridine, β-picoline and NaN₃ in methanol solutions. The electronic structures of the obtained complexes have been calculated using the DFT/TD-DFT method. The trans effect of triphenylphosphine on the pyridine molecule has been studied using NBO and molecular orbital terms, and impact of the acceptor properties of the halide/pseudohalide co-ligands was indicated.     

Synthesis and luminescence properties of hybrid systems based on liquid crystal terbium(ІІІ) and europium(ІІІ) complexes

Russian Journal of General Chemistry - Hybrid liquid crystal systems with different ratios of the components have been prepared on the basis of 5,5′-di(heptadecyl)-2,2′-bipyridine...     

X-ray crystal structure,spectral and magnetic properties of end-to-end di-μ-thiocyanatobis(imidazole)M(II) polymeric complexes (M=Co,Mn): supramolecular network structure based on N–H ··· S hydrogen bonding and π ··· π stacking

Two isomorphous one-dimensional chain complexes Co(NCS)₂(Him)₂ (1) and Mn(NCS)₂(Him)₂ (2) (Him?=?imidazole) have been prepared and characterized structurally. Both 1 and 2 crystallize in the monoclinic system, space group P2₁/n, and the structures consist of one-dimensional polymeric chains in which metal ions are bridged by two thiocyanate groups bonding in end-to-end fashion. Both 1 and 2 exhibit two-dimensional sheet structures with N–H?···?S hydrogen bonds and three-dimensional supramolecular network structure with π?···?π stacking interactions. IR spectra indicate the presence of bridging thiocyanate groups in both 1 and 2, confirmed by their structures. The variable temperature magnetic susceptibility, measured in the 2–300?K range, indicates weak antiferromagnetic exchange interactions in complex 2.     

Intramolecular MLOH/π and MLNH/π interactions in crystal structures of metal complexes

Intramolecular metal-ligand OH/π (MLOH/π) and metal-ligand NH/π (MLNH/π) interactions in transition metal complexes between aqua or ammine ligand and ligand containing a C6-aromatic ring were investigated in crystal structures deposited in the Cambridge Structural Database (CSD). These intramolecular interactions appear in 38 structures with aqua ligand as the hydrogen atom donor and in 10 structures with ammine ligand as the hydrogen atom donor. Among all these complexes only one is negatively charged, 14 are positively charged and 33 are neutral indicating that the overall charge of the molecule has an influence on the XH/π (X = O or N) interactions. Energy estimated by DFT calculations is approximately 19 kJ mol⁻¹ for the MLOH/π interactions and approximately 15 kJ mol⁻¹ for the MLNH/π interactions. Dedicated to Professor Milan Melník on the occasion of his 70th birthday     

Theoretical study of structural and electronic properties of oligo（thiophene-phenylene）s in comparison with oligothiophenes and oligophenylenes

In this work, a quantum-chemical investigation on the structural and opto-electronic properties of oligo（thiophene-phenylene） （4TP） is carried out. The results are discussed in comparison with the properties of corresponding oligothiophene （8T） and oligophenylene （8P）. As the opto-electronic properties of this type of conducting polymers are governed by their electronic band gap, we shall also present a comparison among HOMO, LUMO and band gap energies of these three materials.     

On the weakly C-H···π hydrogen bonded complexes of sevoflurane and benzene

A vibrational assignment of the anaesthetic sevoflurane, (CF(3))(2)CHOCH(2)F, is proposed and its interaction with the aromatic model compound benzene is studied using vibrational spectroscopy of supersonic jet expansions and of cryosolutions in liquid xenon. Ab initio calculations, at the MP2/cc-pVDZ and MP2/aug-cc-pVDZ levels, predict two isomers for the 1?:?1 complex, one in which the near-cis, gauche conformer of sevoflurane is hydrogen bonded through its isopropyl-hydrogen atom, the other in which the same conformer is bonded through a bifurcated hydrogen bond with the fluoromethyl hydrogen atoms. From the experiments it is shown that the two isomers are formed, however with a strong population dominance of the isopropyl-bonded species, both in the jet and liquid phase spectra. The experimental complexation enthalpy in liquid xenon, ΔH(o)(LXe), of this species equals -10.9(2) kJ mol(-1), as derived from the temperature dependent behaviour of the cryosolution spectra. Theoretical complexation enthalpies in liquid xenon were obtained by combining the complete basis set extrapolated complexation energies at the MP2/aug-cc-pVXZ (X = D,T) level with corrections derived from statistical thermodynamics and Monte Carlo Free Energy Perturbation calculations, resulting in a complexation enthalpy of -11.2(3) kJ mol(-1) for the isopropyl-bonded complex, in very good agreement with the experimental value, and of -11.4(4) kJ mol(-1), for the fluoromethyl-bonded complex. The Monte Carlo calculations show that the solvation entropy of the isopropyl-bonded species is considerably higher than that of the fluoromethyl-bonded complex, which assists in explaining its dominance in the liquid phase spectra.     

Theoretical investigation study based on PM3MM and ONIOM2 calculations of β-Cyclodextrin complexes with diphenylamine

The inclusion complex of β-cyclodextrin (β-CD) and diphenylamine (DPA) was investigated by using PM3MM, DFT, HF and ONIOM2 methods. The most stable structure was obtained at the optimum position and angle. The results indicate that the inclusion complex formed by DPA entering into the cavity of β-CD from its wide side (the secondary hydroxyl group side) is more stable than that formed by DPA entering into the cavity of β-CD from its narrow side (the primary hydroxyl group side). The structures show the presence of several intermolecular hydrogen bond interactions that were studied on the basis of natural bonding orbital (NBO) analysis, employed to quantify the donor–acceptor interactions between diphenylamine and β-CD. A study of these complexes in solution was carried out using the CPCM model to examine the influence of solvation on the stability of the diphenylamine β-CD complex.     

Theoretical studies on the electronic structures and spectroscopic properties for a series of Osmium(II)-2,2′,6′,2′′-terpyridine complexes

A series of Osmium(II) complexes [Os (trpy-R)₂]²⁺(trpy=2,2′,6′,2′′-terpyridine and R=H (1), OH (2), and C₆H₅(3)) have been investigated by the density functional (DF) and ab initio calculations. The structures of 1–3 in the ground and excited states were fully optimized at the B3LYP and CIS level, respectively, and their absorption and emission spectra in the acetonitrile solution were obtained using the TD-DFT (B3LYP) method associated with the PCM model. The calculations indicated that, for 1–3, the variation of the substituents on the terpyridine ligand only slightly changes their geometrical structures in the ground and excited states but leads to a sizable difference in the electronic structures. The results show that the low-lying MLCT/ILCT transitions (at 446 (1), 465 (2), and 499 nm (3)) are red-shifted according to the electron-donating ability of substituents on the terpyridine ligand, but blue-shift trend of the high-lying ILCT transitions (at 301 (1), 297 (2), and 272 nm (3)). It also reveals that the lowest energy emissions of 1–3 at 649 nm, 656 nm, and 676 nm have the character of mixing ³[π*(trpy) → d(Os)] and ³ ππ* (³MLCT/³ILCT) transitions localized on the terpyridine ligand, which are identical to the transition properties of the lowest-energy absorptions.     

Theoretical studies on the spectroscopic properties and the substituent effects of pyridyl triazole Os(Ⅱ) complexes

To explore the spectroscopic properties of pyridyl triazole Os(Ⅱ) complexes and how the substituent effects affect the spectroscopic properties of [Os(ptz)2L2] (L=PH3; ptzH=(2-pyridyl)-1,2,4-triazole) (1), [Os(bptz)2L2] (bptzH=3-tert-butyl-5-(2-pyridyl)-1,2,4-triazole) (2), [Os(fptz)2L2] (fptzH=3- (trifluoreomethyl)- 5-(2-pyridyl)-1,2,4-triazole) (3), and [Os(fbtz)2L2] (fbtzH=3-(trifluoreomethyl)-5-(4-tert-butyl- 2-pyridyl)-1,2, 4-triazole) (4), the density functional theory (DFT) method at the B3LYP level ...     

Coordination bonding in dicopper and dichromium tetrakis(μ-acetato)-diaqua complexes: Nature,strength, length,and topology

Geometry optimization, energetics, electronic structure, and topology of electron density of dicopper ( I ) and dichromium ( II ) tetrakis(μ-acetato)-diaqua complexes are studied focusing on the metal–metal interactions. The performance of broken symmetry (BS) single-determinant ab initio (Hartree–Fock, Møller–Plesset perturbation theory to the second and third orders, coupled clusters singles and doubles) and density functional theory (BLYP, B3LYP, B3LYP-D3, B2PLYP, MPW2PLYP) methods is compared to multideterminant ab initio (CASSCF, NEVPT2) methods as well as to the multipole model of charge density from a single-crystal X-ray diffraction experiment (Herich et al., Acta Cryst. 2018, B74, 681–692). In vacuo DFT geometry optimizations (improper axial water ligand orientation) are compared against the periodic ones. The singlet state is found to be energetically preferred. J coupling of ( I ) becomes underestimated for all ab initio methods used, when compared to experiment. It is concluded that the strength of the direct M─M interactions correlates closely with the J coupling magnitude at a given level of theory. The double potential well character of (II) and of the dehydrated form of (II) are considered with respect to the Cr─Cr distance. The physical effective bond order of the metal–metal interaction is small (below 0.1 e) in ( I ) and moderate (0.4 e) in ( II ). The CASSCF results overestimate the electron density of the metal–metal bond critical point by 20% and 50% in ( I ) and ( II ), respectively, when compared to the multipole model. © 2019 Wiley Periodicals, Inc.     

Watson–Crick versus imidazopyridopyrimidine base pairs: theoretical study on differences in stability and hydrogen bonding strength

Matsuda and coworkers demonstrated that imidazopyridopyrimidine nucelobases (N ^N , O ^O , N ^O , tO ^O , and O ^N ) can mimic Watson–Crick nucleobase in forming H-bonds in DNA double helix. In the present study, we address the question about the strengths of the H-bonds in imidazopyridopyrimidine base pairs compared to those in Watson–Crick ones by focusing particularly on the nature of these interactions. Optimized structures of imidazopyridopyrimidine, imidazopyridopyrimidine–Watson–Crick, and Watson–Crick base pairs are obtained at the DFTB3LYP/6-311++G (d,p). The nature and strength of the intramolecular H-bonds in these base pairs have been investigated based on natural bond orbital (NBO method) to consider the effect of charge transfer, “atoms-in-molecules” (AIM) topological parameters, and decomposition of the interaction energies using the energy decomposition analysis (EDA). These investigations imply that N ^N –O ^O and N ^O –O ^N can form base pairs with four H-bonds (most stable than those of Watson–Crick base pairs) when they incorporated into DNA double helix. Furthermore, it can be deduced that O ^N and N ^N nucleobases form energetically more favorable pairs with adenine and guanine than the normal Watson–Crick counter parts. These results can be helpful for the stabilization and regulation of a variety of new base-pairing motif of DNA structures.