Substituent effects in hydrogen bonding: DFT and QTAIM studies on acids and carboxylates complexes with formamide.
Ontology highlight
ABSTRACT:
SUBMITTER: Osmialowski B
PROVIDER: S-EPMC4139586 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Next-generation quantum theory of atoms in molecules (QTAIM) was used to investigate the competition between hydrogen bonding and halogen bonding for the recently proposed (Y = Br, I, At)/halogenabenzene/NH3 complex. Differences between using the SR-ZORA Hamiltonian and effective core potentials (ECPs) to account for relativistic effects with increased atomic mass demonstrated that next-generation QTAIM is a much more responsive tool than conventional QTAIM. Subtle details of the competition between halogen bonding and hydrogen bonding were observed, indicating a mixed chemical character shown in the 3-D paths constructed from the bond-path framework set B. In addition, the use of SR-ZORA reduced or entirely removed spurious features of B on the site of the halogen atoms.
| S-EPMC6720212 | biostudies-literature
Project description:Adenine, one of the components of DNA/RNA helices, has the ability to form self-organizing structures with cyclic hydrogen bonds (A4), similar to guanine quartets. Here, we report a computational investigation of the effect of substituents (X = NO2, Cl, F, H, Me, and NH2) on the electronic structure of 9H-adenine and its quartets (A4-N1, A4-N3, and A4-N7). DFT calculations were used to show the relationships between the electronic nature of the substituents, strength of H-bonds in the quartets, and aromaticity of five- and six-membered rings of adenine. We demonstrated how the remote substituent X modifies the proton-donating properties of the NH2 group involved in the H-bonds within quartets and how the position of the substituent and its electronic nature affect the stability of the quartets. We also showed the possible changes in electronic properties of the substituent and aromaticity of adenine rings caused by tetramer formation. The results indicate that the observed relationships depend on the A4 type. Moreover, the same substituent can both strengthen and weaken intermolecular interactions, depending on the substitution position.
| S-EPMC9054646 | biostudies-literature
Project description:Sulfated cellulose derivatives are biologically active substances with anticoagulant properties. In this study, a new sulfated diethylaminoethyl (DEAE)-cellulose derivative has been obtained. The effect of a solvent on the sulfation process has been investigated. It is shown that 1,4-dioxane is the most effective solvent, which ensures the highest sulfur content in DEAE-cellulose sulfate under sulfamic acid sulfation. The processes of sulfamic acid sulfation in the presence of urea in 1,4-dioxane and in a deep eutectic solvent representing a mixture of sulfamic acid and urea have been compared. It is demonstrated that the use of 1,4-dioxane yields the sulfated product with a higher sulfur content. The obtained sulfated DEAE-cellulose derivatives have been analyzed by Fourier transform infrared spectroscopy, X-ray diffractometry, and scanning electron and atomic force microscopy, and the degree of their polymerization has been determined. The introduction of a sulfate group has been confirmed by the Fourier transform infrared spectroscopy data; the absorption bands corresponding to sulfate groups have been observed in the ranges of 1247-1256 and 809-816 cm-1. It is shown that the use of a deep eutectic solvent leads to the side carbamation reactions. Amorphization of DEAE-cellulose during sulfation has been demonstrated using X-ray diffractometry. The geometric structure of a molecule in the ground state has been calculated using the density functional theory with the B3LYP/6-31G(d, p) basis set. The reactive areas of DEAE-cellulose and its sulfated derivatives have been analyzed using molecular electrostatic potential maps. The thermodynamic parameters (heat capacity, entropy, and enthalpy) of the target sulfation products have been determined. The HOMO-LUMO energy gap, Mulliken atomic charges, and electron density topology of the title compound have been calculated within the atoms in molecule theory.
| S-EPMC8427635 | biostudies-literature
Project description:In this manuscript, we combined ab initio calculations (RI-MP2/def2-TZVPD level of theory) and a search in the CSD (Cambridge Structural Database) to analyze the influence of aromatic substitution in charge-assisted multivalent halogen bonding complexes. We used a series of benzene substituted iodine derivatives C₆H₄(IF₄)Y (Y = H, NH₂, OCH₃, F, CN, and CF₃) as Lewis acids and used Cl- as electron rich interacting atoms. We have represented the Hammett's plot and observed a good regression coefficient (interaction energies vs. Hammett's σ parameter). Additionally, we demonstrated the direct correlation between the Hammett's σ parameter and the value of molecular electrostatic potential measured at the I atom on the extension of the C-I bond. Furthermore, we have carried out AIM (atoms in molecules) and NBO (natural bonding orbital) analyses to further describe and characterize the interactions described herein. Finally, we have carried out a search in the CSD (Cambridge Structural Database) and found several X-ray structures where these interactions are present, thus giving reliability to the results derived from the calculations.
| S-EPMC5943962 | biostudies-literature
Project description:Alfred Werner described the attributes of the primary and secondary coordination spheres in his development of coordination chemistry. To examine the effects of the secondary coordination sphere on coordination chemistry, a series of tripodal ligands containing differing numbers of hydrogen bond (H-bond) donors were used to examine the effects of H-bonds on Fe(II), Mn(II)-acetato, and Mn(III)-OH complexes. The ligands containing varying numbers of urea and amidate donors allowed for systematic changes in the secondary coordination spheres of the complexes. Two of the Fe(II) complexes that were isolated as their Bu4N+ salts formed dimers in the solid-state as determined by X-ray diffraction methods, which correlates with the number of H-bonds present in the complexes (i.e., dimerization is favored as the number of H-bond donors increases). Electron paramagnetic resonance (EPR) studies suggested that the dimeric structures persist in acetonitrile. The Mn(II) complexes were all isolated as their acetato adducts. Furthermore, the synthesis of a rare Mn(III)-OH complex via dioxygen activation was achieved that contains a single intramolecular H-bond; its physical properties are discussed within the context of other Mn(III)-OH complexes.
| S-EPMC4043334 | biostudies-literature
Project description:First-principles Car-Parrinello molecular dynamics, ab initio (MP2) and density functional schemes have been used to explore the tautomeric equilibrium in three tris(amino(R)methylidene)cyclohexane-1,3,5-triones (R = hydrogen, methyl or phenyl group). The dynamic nature of the cyclic hydrogen bonding has been studied by the first-principles MD method. The comparison of the results obtained by aforesaid methods has been accomplished on the basis of calculations of structural and spectroscopic characteristics of the compounds. The conformational analysis of the studied compounds has been carried out at the MP2/6-31+G(d,p) and B3LYP/6-31+G(d,p) levels of theory. The influence of steric and electronic effects on the cyclic hydrogen bonding has been analysed. The extent of the proton delocalization has been modified by the substituents according to the sequence: hydrogen < phenyl < methyl. This fact is verified by the spectroscopic and structural data as well as the energy potential curve. A prevalence of the keto-enamine tautomeric form has been observed in the static ab initio and DFT models, and confirmed by the first-principles MD.
| S-EPMC3474916 | biostudies-literature
Project description:Hydrogen bonding (H-bonding) is generally thought to play an important role in tuning the electronic structure and reactivity of metal-sulfur sites in proteins. To develop a quantitative understanding of this effect, S K-edge X-ray absorption spectroscopy (XAS) has been employed to directly probe ligand-metal bond covalency, where it has been found that protein active sites are significantly less covalent than their related model complexes. Sulfur K-edge XAS data are reported here on a series of P450 model complexes with increasing H-bonding to the ligated thiolate from its substituent. The XAS spectroscopic results show a dramatic decrease in preedge intensity. DFT calculations reproduce these effects and show that the observed changes are in fact solely due to H-bonding and not from the inductive effect of the substituent on the thiolate. These calculations also indicate that the H-bonding interaction in these systems is mainly dipolar in nature. The -2.5 kcal/mol energy of the H-bonding interaction was small relative to the large change in ligand-metal bond covalency (30%) observed in the data. A bond decomposition analysis of the total energy is developed to correlate the preedge intensity change to the change in Fe-S bonding interaction on H-bonding. This effect is greater for the reduced than the oxidized state, leading to a 260 mV increase in the redox potential. A simple model shows that E degrees should vary approximately linearly with the covalency of the Fe-S bond in the oxidized state, which can be determined directly from S K-edge XAS.
| S-EPMC2880190 | biostudies-literature
Project description:The hydrogen bond enhanced halogen bond (HBeXB) has recently been used to effectively improve anion binding, organocatalysis, and protein structure/function. In this study, we present the first systematic investigation of substituent effects in the HBeXB. NMR analysis confirmed intramolecular HBing between the amine and the electron-rich belt of the XB donor (N-H⋯I). Gas-phase density functional theory studies showed that the influence of HBing on the halogen atom is more sensitive to substitution on the HB donor ring (R1). The NMR studies revealed that the intramolecular HBing had a significant impact on receptor performance, resulting in a 50-fold improvement. Additionally, linear free energy relationship (LFER) analysis was employed for the first time to study the substituent effect in the HBeXB. The results showed that substituents on the XB donor ring (R2) had a competing effect where electron donating groups strengthened the HB and weakened the XB. Therefore, selecting an appropriate substituent on the adjacent HB donor ring (R1) could be an alternative and effective way to enhance an electron-rich XB donor. X-ray crystallographic analysis demonstrated that intramolecular HBing plays an important role in the receptor adopting the bidentate conformation. Taken together, the findings imply that modifying distal substituents that affect neighboring noncovalent interactions can have a similar impact to conventional para substitution substituent effects.
| S-EPMC10445465 | biostudies-literature
Project description:The ability of gold to act as proton acceptor and participate in hydrogen bonding remains an open question. Here, we report the synthesis and characterization of cationic gold(I) complexes featuring ditopic phosphine-ammonium (P,NH+) ligands. In addition to the presence of short Au∙∙∙H contacts in the solid state, the presence of Au∙∙∙H-N hydrogen bonds was inferred by NMR and IR spectroscopies. The bonding situation was extensively analyzed computationally. All features were consistent with the presence of three-center four-electron attractive interactions combining electrostatic and orbital components. The role of relativistic effects was examined, and the analysis is extended to other recently described gold(I) complexes.
| S-EPMC6320517 | biostudies-other
Project description:The combined utility of many one and two dimensional NMR methodologies and DFT-based theoretical calculations have been exploited to detect the intramolecular hydrogen bond (HB) in number of different organic fluorine-containing derivatives of molecules, viz. benzanilides, hydrazides, imides, benzamides, and diphenyloxamides. The existence of two and three centered hydrogen bonds has been convincingly established in the investigated molecules. The NMR spectral parameters, viz., coupling mediated through hydrogen bond, one-bond NH scalar couplings, physical parameter dependent variation of chemical shifts of NH protons have paved the way for understanding the presence of hydrogen bond involving organic fluorine in all the investigated molecules. The experimental NMR findings are further corroborated by DFT-based theoretical calculations including NCI, QTAIM, MD simulations and NBO analysis. The monitoring of H/D exchange with NMR spectroscopy established the effect of intramolecular HB and the influence of electronegativity of various substituents on the chemical kinetics in the number of organic building blocks. The utility of DQ-SQ technique in determining the information about HB in various fluorine substituted molecules has been convincingly established.
| S-EPMC6155419 | biostudies-other