Proton Donor Bonds Research Articles

Self-associates of 1,2,4-triazole: FTIR studies, quantum chemical calculations and topological analysis

The Fourier Transform Infrared (FTIR) spectroscopic technique has been employed to study the self-associates of 1,2,4-triazole (Htrz) in solid phase. The self-associates have been identified using density functional theory (DFT) calculations carried out on various multimers of Htrz under B3LYP/6–311++ G(d, p) level. Comparison of the experimental and theoretical frequencies of N−H andC−Hstretching absorptional bands indicate that Htrz exists as multimers upto hexamer. The Occupancy of the anti-bonding orbitals of the proton donors, Natural bond Orbital (NBO), Frontier Molecular Orbital (FMO), Electrostatic potential surface (ESP), reduced density gradient (RDG) analyses have also been executed. In addition, topological parameters have also been analysed to characterize the hydrogen bonds and proton donating covalent bonds. The analyses show that pentamer is the most stable among all the H-bonded associates and the dimer 3 in which classical and non-classical H-bond interaction coexists is the least stable. The topological parameter values suggest that the N−H bonds of dimer1/pentamer are with the highest/smallest covalent character. The criteria proposed in literature to describe the covalent nature of bonds, in particular proton donor bonds, appears to fails in the Htrz dimer in which classical and non-classical hydrogen bonds coexist.

Um Estudo Químico-quântico da Covalência Intermolecular em Sistemas Estabilizados por Ligações de Hidrogênio π∙∙∙H e N∙∙∙H: Cálculos DFT, ChelpG, NBO e QTAIM

In this work, density functional calculations at BHandHLYP/6-311++G(d,p) theoretical level of structural parameters, electronic properties and vibration modes of the C 2 H 2 ∙∙∙HCN∙∙∙HF and C 2 H 4 ∙∙∙HCN∙∙∙HF T-shaped hydrogen complexes is presented. As is well-known, the formation of these complexes is ruled by weak and strong hydrogen bonds recognized as p∙∙∙H and N∙∙∙H, respectively. In line with this interaction strength, a correlation between the structural modifications and frequency shifts was investigated, although the non-covalent character of these complexes has been unveiled through the QTAIM calculations. The absorption intensity ratios of the proton donors correlate well with the charge transfer amounts, whose values were computed through the ChelpG approach. Even by taking into account the cooperative profile of these systems, the hydrogen bond energies were determined, and actually, the values are unapproachable to be distributed in different moieties, such as punctual strong hydrogen bonds possessing covalent character, if exist. At last, the NBO calculations were applied to compute the s - and p -contributions on the hybrid orbitals in order to explain the frequency shifts on the H–C and H–F proton donor bonds. DOI: http://dx.doi.org/10.17807/orbital.v1i1.705

The structures of heterocyclic complexes ruled by hydrogen bonds and halogen interactions: Interaction strength and IR modes

In this work, the existence of multiple interactions in heterocyclic complexes of C2H4O⋯nHCCl3 and C2H4S⋯nHCCl3 with n=2 and 3 was unveiled at the B3LYP/6-311++G(d,p) level of theory. The forward analyses of the vibrational spectra revealed the appearing of red-shifts in the H−C bond. In agreement with this and through the optimized geometries of these systems, an increase in the H−C bond length was also observed. Besides O⋯H and S⋯H, other hydrogen bonds formed between chlorine⋯hydrogen and mainly the halogen interactions formed by chlorine⋯chlorine were identified. Thereby, the vibration spectra of the heterocyclic complexes were reanalyzed with the purpose to locate new red-shifts, although only those characterized in H−C have been detected up to then. In addition to the correlation between the frequencies shifted to downward values followed by increases in the bond lengths, the interpretation of the red-shifts was conducted by means of the Bent rule of the hybridization theory. The interaction strength was examined in several viewpoints, and one of them was the relationship between the H-bond energies and the intermolecular electronic density computed by means of the Quantum Theory of Atoms in Molecules (QTAIM). Moreover, the prediction of the interaction strength was also made through the combination between vibration modes (red-shifts) and variation of topological parameters, such as the electronic density and Laplacian of the proton donor bond (C−H).

A theoretical perspective of the nature of hydrogen-bond types – the atoms in molecules approach

Hydrogen bonds and their strength were analysed based on their X–H proton–donor bond properties and the parameters of the H–Y distance (Y proton acceptor). Strong, moderate and weak interactions in hydrogen-bond types were verified through the proton affinities of bases (PA), deprotanation enthalpies of acids (DPE) and the chemical shift (σ). The aromaticity and anti-aromaticity were analysed by means of the NICS (0) (nucleus-independent chemical shift), NICS (1) and ΔNICS (0), ΔNICS (1) of hydrogen-bonded molecules. The strength of a hydrogen bond depends on the capacity of hydrogen atom engrossing into the electronegative acceptor atom. The correlation between the above parameters and their relations were discussed through curve fitting. Bader's theory of atoms in molecules has been applied to estimate the occurrence of hydrogen bonds through eight criteria reported by Popelier et al. The lengths and potential energy shifts have been found to have a strong negative linear correlation, whereas the lengths and Laplacian shifts have a strong positive linear correlation. This study illustrates the common factors responsible for strong, moderate and weak interactions in hydrogen-bond types.

Hydrogen bonds determine the structures of the ternary heterocyclic complexes C2H4O···2HF, C2H5N···2HF and C2H4S···2HF: density functional theory and topological calculations

A theoretical study of structural, electronic, topological and vibrational parameters of the ternary hydrogen-bonded complexes C(2)H(4)O···2HF, C(2)H(5)N···2HF and C(2)H(4)S···2HF is presented here. Different from binary systems with a single proton donor, the tricomplexes have the property of forming multiple hydrogen bonds, which are analyzed from a structural and vibrational point of view, but verified only by means of the quantum theory of atoms in molecules (QTAIM). As traditionally done in the hydrogen bond theory, the charge transfer between proton donors and acceptors was computed using the CHELPG calculations, which also revealed agreement with dipole moment variation and a cooperative effect on the tricomplexes. Furthermore, redshift events on proton donor bonds were satisfactorily identified, although, in this case, an absence of experimental data led to the use of a theoretical argument to interpret these spectroscopic shifts. It was therefore the use of the QTAIM parameters that enabled all intermolecular vibrational modes to be validated. The most stable tricomplex in terms of energy was identified via the strength of the hydrogen bonds, which were modeled as directional and bifurcated.

Understanding the Population, Coordination, and Orientation of Water Species Contributing to the Nonlinear Optical Spectroscopy of the Vapor−Water Interface through Molecular Dynamics Simulations

Molecular dynamics simulations are used to deconvolve the vibrational spectral features of the vapor-water interface based on molecular environment. A simple geometric description of hydrogen bonding is deployed to identify the OH stretch modes that comprise the vibrational sum-frequency spectrum of the vapor-water interface with direct comparison to our experimental results. The population densities of different species of water molecules are presented as functions of interfacial depth and orientation. It is found that surface water molecules that possess one proton donor bond and one proton acceptor bond make the dominant contribution to both the SSP- and SPS-polarized spectral responses and are located within an angstrom of the Gibbs dividing surface.

Interaction with Glycine Increases Stability of a Mutagenic Tautomer of Uracil. A Density Functional Theory Study

The most stable structures for the gas-phase complexes of minor tautomers of uracil (U) with glycine (G) were characterized at the density functional B3LYP/6-31++G level of theory. These are cyclic structures stabilized by two hydrogen bonds. The relative stability of isolated tautomers of uracil was rationalized by using thermodynamic and structural arguments. The stabilization energies for complexes between the tautomers of U and G result from interplay between the stabilizing two-body interaction energies and destabilizing one-body terms. The latter are related to the energies of (i) tautomerization of the unperturbed moieties and (ii) distortions of the resulting rare tautomers in the complex. The two-body term describes the interaction energy between distorted tautomers. The two-body interaction energy term correlates with perturbations of length of the proton-donor bonds as well as with deprotonation enthalpies and proton affinities of the appropriate monomer sites. It was demonstrated that the relative instability of rare tautomers of uracil is diminished due to their interactions with glycine. In particular, the instability of the third most stable tautomer (U(III)) is decreased from 11.9 kcal/mol for non-interacting uracil to 6.7 kcal/mol for uracil in a complex with the zwitterionic tautomer of glycine. A decrease of instability by 5.2 kcal/mol could result in an increase of concentration of U(III) by almost 5 orders of magnitude. This is the tautomer with proton donor and acceptor sites matching guanine rather than adenine. Moreover, kinetic characteristics obtained for the glycine-assisted conversion of the most stable tautomer of uracil (U(I)) to U(III) indicate that the U(I)<-->U(III) thermodynamic equilibrium could be easily attained at room temperature. The resulting concentration of this tautomer falls in a mutationally significant range.

Computational Study of Hydrogen-Bonded Complexes between the Most Stable Tautomers of Glycine and Uracil

A total of 23 hydrogen bonded complexes between the lowest energy tautomers of uracil and glycine have been characterized at the density functional level of theory with a hybrid B3LYP exchange-correlation functional and 6-31++G** basis sets. The most stable complexes are formed when the carboxylic group of glycine is bound through two hydrogen bonds with a NH proton donor and an O proton acceptor of uracil, and stabilization energies for these cyclic structures span a range of 12.3−15.6 kcal/mol. Interplay between the topological match among proton donor and acceptor sites involved in cyclic structures and their preference to form single hydrogen bonds, measured by the values of proton affinity and deprotonation enthalpy, has been discussed. Upon formation of a uracil−glycine complex, the elongations of proton donor bonds and vibrational red shifts for proton donor stretching modes can reach 0.05 A and 650 cm-1, respectively. These perturbations of proton donor bonds correlate with the magnitude of two-bo...

Characterization of Hydrogen Bonding in a Continuum Solvent Model

A simple approach for calculating hydrogen bonding (H-bonding) effects in molecular mechanics simulations of peptides and proteins is presented for use in the framework of the continuum solvent model described in the previous paper. In this approach, the solvated macromolecule is treated as a three-component dielectric system consisting of the solvent, bulk protein, and proton acceptor media. The hydrogen bond (H-bond) interaction is identified from the interpenetration of the van der Waals spheres of the polar hydrogen and the proton acceptor. The H-bond geometry is characterized by the ideal orientation of the electron lone pairs in the acceptor atom and the directionality of the proton donor bond, as observed in experimental and ab initio studies, and classified according to the hybridization state of the acceptor atom. The algorithm was implemented into CHARMM using the PAR22 force field. By introducing the concept of a Born radius of a polar hydrogen immersed in an acceptor environment, the stabiliza...

The nature of hydrogen bonding

Published work on spectroscopic and theoretical investigations of hydrogen bondingare reviewed (eighty references). This evidence is discussed and the conclusion that the quantum contribution to hydrogenbonding is of major importance leads to three criteria for hydrogen bond formation.(a) Partially ionic proton donor bond (b) Asymmetric lone pair orbitals on proton acceptor.(c) X-H bond and lone pair orbital collinear. The extreme broadening of the OH stretching vibration band has many possible contributorymechanisms, but proton transfer across the bond from the vibrationally excited -X-H maymake the major contribution.