Individual Hydrogen Bonds Research Articles

Hydration of selenolate moiety: Ab initio investigation of properties of O-H⋯Se(-) hydrogen bonds in CH3 Se(-)⋯(H2 O)n clusters.

This work is devoted to investigations of the influence of O-H···Se(-) hydrogen bonds on the electronic shells of selenolate R-Se(-) fragment (R═CH3 ). The geometric, energetic and nuclear magnetic resonance (NMR) spectral parameters for various conformers of CH3 Se(-)⋯(H2 O)n clusters with n=0-6 were calculated at CCSD/aug-cc-pVDZ level of theory. For selenolate anion CH3 Se(-) solvation free energy was calculated, and for water media it is equal to -71.41 kcal/mol. For O-H···Se(-) hydrogen bonds the proportionality coefficients between QTAIM parameters at (3; -1) bond critical point and the strength of an individual hydrogen bond ∆E were proposed. It was shown, that despite a relative weakness of O-H···Se(-) hydrogen bonds, the outer electronic shell of the selenium atom changes significantly upon formation of each hydrogen bond. This, in turn, cause the dramatic change of NMR parameters of selenium nuclei.

How can fluorine directly and indirectly affect the hydrogen bonding in molecular systems? – A case study for monofluoroanilines

Hydrogen bonds (HBs) directly engaging fluorine has been extensively studied, but the indirect effect of fluorine on adjacent donors and acceptors is poorly understood and still difficult to predict. The indirect and direct effect of the fluorination of aniline on HB patterns observed in monofluoroanilines was studied via experimental (vibrational spectroscopy and crystal structure analysis) and theoretical (ab initio molecular dynamics and electrostatic surface potential) methods. It was found that a fluorine substituent decreases the strength and frequency of N–H⋯N HBs and, at the same time, increases the acidity of CH protons, enhancing the competitiveness of weaker interactions. Additionally, the position of fluorine in the aromatic ring strongly affects the C–F bond length, and a direct intramolecular N–H⋯F HB causes an increase in the N–H bond stability. We also provide a methodology to identify and separate individual HBs concerning the type of donor or acceptor from the ab initio molecular dynamics trajectories.

Appraisal of individual hydrogen bond strengths and cooperativity in ammonia clusters via a molecular tailoring approach.

In this work, we propose and test a method, based on the molecular tailoring approach (MTA), for the evaluation of individual hydrogen bond (HB) energies in ammonia (NH3)n clusters. This methodology was tested, in our earlier work, on water clusters. Liquid ammonia being a universal, non-aqueous ionizing solvent, such information of individual HB strength is indispensable in many studies. The estimated HB energies by an MTA-based method, in (NH3)n for n = 3-8, were calculated to be in the range of 0.65 to 5.54 kcal mol-1 with the cooperativity contribution falling between -0.54 and 1.88 kcal mol-1 both calculated at the MP2(full)/aug-cc-pVTZ level of theory. It is seen that the strong HBs in (NH3)n clusters were additionally strengthened by the large contribution of HB cooperativity. The accuracy of these estimated HB energies was validated by approximately estimating the molecular energy of a given cluster by adding the sum of HB energies to the sum of monomer energies. This approximately estimated molecular energy of a given cluster was found to be in excellent agreement with the actual calculated values. The negligibly small difference (less than 5.6 kcal mol-1) in these two values suggests that the estimated individual HB energies in ammonia clusters are quite reliable. Furthermore, these estimated HB energies by MTA are in excellent qualitative agreement with the other indirect measures of HB strength, such as HB bond distances and angles, N-H stretching frequency and the electron density values at the (3,-1) bond critical points.

Variable temperature FTIR spectra of polycrystalline purine nucleobases and estimating strengths of individual hydrogen bonds

In the first part of this work, we report the FTIR spectra of pure NH and isotopically substituted ND (10–15% D and 80–90% D) polycrystalline hypoxanthine, xanthine, adenine and guanine recorded in the 400–4000 cm−1 range, as a function of temperature (10–300 K). We provide assignments of the stretching and out-of-plane bending amine (NH2) and imine (NH) bands to the distinct H-bonds present in the crystal, based on the temperature sensitivity and isotopic exchange behavior. Empirical correlations between spectral and thermodynamic or structural parameters enabled us to estimate the energies and lengths of H-bonds in the studied nucleobase crystals and to correlate them with literature data. The empirical H-bonding energies are compared with H-bonding and stacking energies computed for hypoxanthine.In the second part, strategies for using the empirical correlations together with information extracted from quantum mechanical data (in particular from the Bader’s quantum theory of atoms in molecules, QTAIM) for the evaluation of hydrogen bonding properties are discussed, and their advantages and drawbacks pointed out. The justification for a cooperative use of quantum-mechanical calculations with empirical spectra-energy correlations is discussed.

Connecting the Stimuli-Responsive Rheology of Biopolymer Hydrogels to Underlying Hydrogen-Bonding Interactions.

Many biopolymer hydrogels are environmentally responsive because they are held together by physical associations that depend on pH and temperature. Here, we investigate how the pH and temperature responses of the rheology of hyaluronan hydrogels are connected to the underlying molecular interactions. Hyaluronan is an essential structural biopolymer in the human body with many applications in biomedicine. Using two-dimensional infrared spectroscopy, we show that hyaluronan chains become connected by hydrogen bonds when the pH is changed from 7.0 to 2.5 and that the bond density at pH 2.5 is independent of temperature. Temperature-dependent rheology measurements show that because of this hydrogen bonding the stress relaxation at pH 2.5 is strongly slowed down in comparison to pH 7.0, consistent with the sticky reptation model of associative polymers. From the flow activation energy, we conclude that each polymer is cross-linked by multiple (5–15) hydrogen bonds to others, causing slow macroscopic stress relaxation, despite the short time scale of breaking and reformation of each individual hydrogen bond. Our findings can aid the design of stimuli-responsive hydrogels with tailored viscoelastic properties for biomedical applications.

Supramolecular architectures of Mn(NCS)2 complexes with N'-(1-(pyridin-4-yl)ethylidene)picolinohydrazide and N'-(phenyl(pyridin-4-yl)methylene)isonicotinohydrazide

In this work we have synthesized and characterized new mononuclear heteroleptic discrete complexes [Mn(NCS)2(HLI)2(MeOH)2] (1), [Mn(NCS)2(HLI)2(EtOH)2] (2) and [Mn(NCS)2(HLII)2(EtOH)2] (3), fabricated from Mn(NCS)2 and N'-(1-(pyridin-4-yl)ethylidene)picolinohydrazide (HLI) and N'-(phenyl(pyridin-4-yl)methylene)isonicotinohydrazide (HLII) in MeOH or EtOH. All the obtained complexes are structurally similar, while complexes 1 and 2 are isostructural. The metal center in all the structures is six-coordinated and in a N4O2 geometry, formed by two monodentate ligands HLI or HLII, each exclusively linked through the 4-pyridil nitrogen atom, two N-coordinated NCS− anions and two O-coordinated molecules of MeOH or EtOH. Crystal packing of 1 and 2 are mainly dictated by the intermolecular OH∙∙∙O hydrogen bonds, while the crystal packing of 3 is mainly driven by the intermolecular OH∙∙∙N hydrogen bonds. The structures of 1–3 reveal the uninodal 1D chains with the 2C1 topology, when complex molecules are considered as a node and OH∙∙∙O (in 1 and 2) of OH∙∙∙N (in 3) hydrogen bonds are considered. Considering remaining non-covalent interactions, the resulting topology can be extended up to a four-connected uninodal sql (Shubnikov tetragonal plane net) topology. The multilevel topological description of the molecular packing of 1–3, when all van der Waals interactions are considered, reveal that the structures of 1 and 2 are assembled from a linear chain through square lattice to different 3D frameworks, while the structure of 3, although starts from the same linear chain, produces 3D frameworks skipping 2D topologies. Molecular surfaces of 1–3 are mainly described by intermolecular H∙∙∙H, H∙∙∙C, H∙∙∙N, H∙∙∙O and H∙∙∙S contacts. Self-assembled supramolecular dimers observed in the solid state of all compounds have been studied using density functional theory (DFT) calculations, molecular electrostatic potential (MEP) surfaces and the NCIplot index. Moreover, the interaction energy of each individual hydrogen bond has been estimated using the quantum theory of «atoms-in-molecules» (QTAIM).

Effect of Alkali Metal Cations on Length and Strength of Hydrogen Bonds in DNA Base Pairs.

For many years, non-covalently bonded complexes of nucleobases have attracted considerable interest. However, there is a lack of information about the nature of hydrogen bonding between nucleobases when the bonding is affected by metal coordination to one of the nucleobases, and how the individual hydrogen bonds and aromaticity of nucleobases respond to the presence of the metal cation. Here we report a DFT computational study of nucleobase pairs interacting with alkali metal cations. The metal cations contribute to the stabilization of the base pairs to varying degrees depending on their position. The energy decomposition analysis revealed that the nature of bonding between nucleobases does not change much upon metal coordination. The effect of the cations on individual hydrogen bonds were described by changes in VDD charges on frontier atoms, H-bond length, bond energy from NBO analysis, and the delocalization index from QTAIM calculations. The aromaticity changes were determined by a HOMA index.

Anion-Anion Complexes Established between Aspartate Dimers.

Stable dimers aspartate-aspartate have been studied in aqueous and gas phase through theoretical simulations. The polarizable continuum model (PCM) has been applied to simulate the effect of the hydration on monomers and complexes. The quantum theory of atoms in molecules (QTAIM) and the interacting quantum atoms (IQA) scheme has been used to inquire into if, in the aqueous phase, individual hydrogen bonds have attractive electrostatic components. In all cases a spontaneous formation of the complexes in the aqueous phase are observed, while in the gas phase a considerable energy barrier must be overcome (between 100.8 to 263.2 kJ mol-1 ). The intermolecular distance at which this barrier is indicates when the hydrogen-bond interactions begin to take importance between the dimers and the corresponding molecular recognition among them. The IQA analysis shows that in aqueous phase, the hydrogen bonds N-H⋅⋅⋅O are mainly electrostatic in nature with a certain covalent character which increases linearly with the decrease of internuclear distances H⋅⋅⋅O. The H⋅⋅⋅H interactions observed are stabilizing and they are mainly quantum in nature.

Infrared intensity analysis of hydroxyl stretching modes in carboxylic acid dimers by means of the charge-charge flux-dipole flux model.

The Charge-Charge Flux-Dipole Flux (CCFDF) model in terms of multipoles from the quantum theory of atoms in molecules (QTAIM) was used to investigate the variations in infrared intensities of hydroxyl (OH) stretching modes during the dimerization of carboxylic acids. The hydrogen bond formation in these systems results into bathochromic shifts of vibrational frequencies for all the OH stretching modes along with huge infrared intensity increments for some of them. These bands become more intense on dimerization due mainly to changes in the cross-term contribution between charge and charge flux. In addition, interaction energies for the pair of atoms directly involved in individual hydrogen bonds (O…H) are linearly correlated to electron densities at their bond critical points (BCPs). Therefore, the hydrogen bonds between the carbonyl group (CO) of acetic acid and the hydroxyl group of halogenated monomers show the largest electron density values at their BCPs. The formation of these intermolecular interactions is also accompanied by ionic character enhancements of OH bonds and electron density decrements at their BCPs. We finally noticed that the hydrogen atom belonging to the hydroxyl group loses electronic charge, while the oxygen from the CO end becomes more negatively charged during dimerization. © 2019 Wiley Periodicals, Inc.

Estimating Strengths of Individual Hydrogen Bonds in RNA Base Pairs: Toward a Consensus between Different Computational Approaches.

Noncoding RNA molecules are composed of a large variety of noncanonical base pairs that shape up their functionally competent folded structures. Each base pair is composed of at least two interbase hydrogen bonds (H-bonds). It is expected that the characteristic geometry and stability of different noncanonical base pairs are determined collectively by the properties of these interbase H-bonds. We have studied the ground-state electronic properties [using density functional theory (DFT) and DFT-D3-based methods] of all the 118 normal base pairs and 36 modified base pairs, belonging to 12 different geometric families (cis and trans of WW, WH, HH, WS, HS, and SS) that occur in a nonredundant set of high-resolution RNA crystal structures. Having addressed some of the limitations of the earlier approaches, we provide here a comprehensive compilation of the average energies of different types of interbase H-bonds (EHB). We have also characterized each interbase H-bond using 13 different parameters that describe its geometry, charge distribution at its bond critical point (BCP), and n → σ*-type charge transfer from filled π orbitals of the H-bond acceptor to the empty antibonding orbital of the H-bond donor. On the basis of the extent of their linear correlation with the H-bonding energy, we have shortlisted five parameters to model linear equations for predicting EHB values. They are (i) electron density at the BCP: ρ, (ii) its Laplacian: ∇2ρ, (iii) stabilization energy due to n → σ*-type charge transfer: E(2), (iv) donor–hydrogen distance, and (v) hydrogen–acceptor distance. We have performed single variable and multivariable linear regression analysis over the normal base pairs and have modeled sets of linear relationships between these five parameters and EHB. Performance testing of our model over the set of modified base pairs shows promising results, at least for the moderately strong H-bonds.

Fine-tuning of Terahertz resonances in hydrogen-bonded organic molecular complexes

Novel organic molecular complexes have been designed and synthesized to obtain prominent Terahertz (THz) resonances in the low-frequency region. Intermolecular hydrogen bonds give rise to low-frequency THz resonances and hence binary organic molecular complexes of pyridyl alkylamide/benzamide (DAP) and hexyl thymine (C6THY) with multiple strong intermolecular hydrogen bonds (NH---O and NH---N) are designed and synthesized. THz resonances of the complexes are fine-tuned by varying the number of benzene rings in the DAP moiety (PrDAP + C6THY, PrPhDAP + C6THY and PhDAP + C6THY). DFT simulation studies of two molecule clusters have been carried out to understand the origin of low-frequency THz resonances. It has been observed that the lowest THz resonances (<2 THz) originate due to translation/rotation of the whole crystal structure and the resonances from 2 to 4 THz are mainly due to intermolecular hydrogen bond bending/stretching vibrations. In order to understand the individual hydrogen bond strengths, compliance constants, which are inverse of the force constants are calculated and Natural Bond Orbital (NBO) analysis has been carried out. Comparison of the experimental THz spectra of different complexes shows that there is a small but tunable variation in THz resonances from one complex to another. Tuning of THz resonances has potential applications in designing THz tags, which can be used in various anti-counterfeiting applications such as currency notes, pharmaceutical tablets.

Theoretical insight to intermolecular hydrogen bond interactions between methyl N-(2-pyridyl) carbamate and acetic acid: substituent effects, cooperativity and energy decomposition analysis

In the present work, the hydrogen bond (HB) interactions between substituted syn and anti rotamers of methyl N-(2-pyridyl) carbamate and acetic acid were investigated using quantum mechanical (QM) calculations. The rotamers have two typical active sites to form hydrogen bonds with acetic acid, such that four stable complexes are found on the potential energy surface. The complexes in which the oxygen atom of carbamate acts as proton acceptor are stabilized by EWSs and are destabilized by EDSs. The trend in the effects of substituents is reversed in the other two complexes, in which the nitrogen atom of ring is involved in the interaction. According to energy data, the substituent effects on the interaction energy can be expressed by Hammett constants. The natural resonance theory (NRT) model was used to investigate the charge distribution on the carbamate group and to discuss the interaction energies. The individual HB energies were estimated to evaluate their cooperative contributions on the interaction energies of the complexes. In addition, the localized molecular orbital energy decomposition analyses (LMO-EDA) demonstrate that the electrostatic interactions are the most important stabilizing components of interactions.

Does the stability of the stacking motif surpass the planar motif in 2-amino-4-nitrophenol? - a CCSD(T) analysis.

In this work we analyzed O-H...O, O-H...N, and N-H...O contacts existing in the 2-amino-4-nitrophenol structure engaged in ANP molecules through quantum chemical methods. Furthermore, the above contacts were favored to comprehensively understand the stability of noncovalent interactions, π stacking and hydrogen bonding, surviving in 2-amino-4-nitrophenol. The geometries of π stacking and hydrogen bond interactions between two 2-amino-4-nitrophenols were optimized at BLYP-D3/def2-QZVP with dispersion 3 and MP2/cc-pVTZ levels of theory, and their stability was compared using the CCSD(T) interaction energies. The analyses predicted a particularly strong π stacking interaction of 2-amino-4-nitrophenol with hydrogen bond due to the narrow equivalent configuration of NO2 interactions with the other 2-amino-4-nitrophenols. Furthermore, this work focused on analyzing the stability of the individual hydrogen bonds existing in planar and stacked arrangements. Graphical abstract Stacked and planar motif in 2-amino-4-nitrophenol.

Quantitative assessment of intermolecular interactions by atomic force microscopy imaging using copper oxide tips.

Atomic force microscopy is an impressive tool with which to directly resolve the bonding structure of organic compounds1-5. The methodology usually involves chemical passivation of the probe-tip termination by attaching single molecules or atoms such as CO or Xe (refs 1,6-9). However, these probe particles are only weakly connected to the metallic apex, which results in considerable dynamic deflection. This probe particle deflection leads to pronounced image distortions, systematic overestimation of bond lengths, and in some cases even spurious bond-like contrast features, thus inhibiting reliable data interpretation8-12. Recently, an alternative approach to tip passivation has been used in which slightly indenting a tip into oxidized copper substrates and subsequent contrast analysis allows for the verification of an oxygen-terminated Cu tip13-15. Here we show that, due to the covalently bound configuration of the terminal oxygen atom, this copper oxide tip (CuOx tip) has a high structural stability, allowing not only a quantitative determination of individual bond lengths and access to bond order effects, but also reliable intermolecular bond characterization. In particular, by removing the previous limitations of flexible probe particles, we are able to provide conclusive experimental evidence for an unusual intermolecular N-Au-N three-centre bond. Furthermore, we demonstrate that CuOx tips allow the characterization of the strength and configuration of individual hydrogen bonds within a molecular assembly.

Direct observation of single-molecule hydrogen-bond dynamics with single-bond resolution

The hydrogen bond represents a fundamental interaction widely existing in nature, which plays a key role in chemical, physical and biochemical processes. However, hydrogen bond dynamics at the molecular level are extremely difficult to directly investigate. Here, in this work we address direct electrical measurements of hydrogen bond dynamics at the single-molecule and single-event level on the basis of the platform of molecular nanocircuits, where a quadrupolar hydrogen bonding system is covalently incorporated into graphene point contacts to build stable supramolecule-assembled single-molecule junctions. The dynamics of individual hydrogen bonds in different solvents at different temperatures are studied in combination with density functional theory. Both experimental and theoretical results consistently show a multimodal distribution, stemming from the stochastic rearrangement of the hydrogen bond structure mainly through intermolecular proton transfer and lactam–lactim tautomerism. This work demonstrates an approach of probing hydrogen bond dynamics with single-bond resolution, making an important contribution to broad fields beyond supramolecular chemistry.

Molecular Dynamics Investigation of the Influence of the Hydrogen Bond Networks in Ethanol/Water Mixtures on Dielectric Spectra.

The dielectric response of fluids to electromagnetic radiation in the microwave region originates from processes occurring at the molecular level. Understanding these processes in more detail is relevant to many fields, such as microwave heating, fluid mixing, and separation technologies. In this work, we use molecular dynamics (MD) simulations to study the dielectric spectra of ethanol/water mixtures. We compare our predictions with experimental results at different compositions. We show how the dielectric response can be estimated to a high level of accuracy using three dielectric relaxations: a dominant and slower process at microwave frequencies and two faster processes. A deeper study of the dynamics of the hydrogen bond network formed in these systems reveals how collective processes between the individual species are the origin of the final dielectric response. Our results agree with the "wait-and-switch" mechanism, which describes the dynamics of the hydrogen bond network as the combination of two processes: the fast breakage and formation of individual hydrogen bonds and the subsequent reorganization of the entire network once this process becomes energetically favorable. Since the dielectric response is related to dipole reorientations in the system, it is directly linked to these mechanisms.

Peroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins.

Copper-hydroperoxido species (CuII-OOH) have been proposed to be key intermediates in biological and synthetic oxidations. Using biotin-streptavidin (Sav) technology, artificial copper proteins have been developed to stabilize a CuII-OOH complex in solution and in crystallo. Stability is achieved because the Sav host provides a local environment around the Cu-OOH that includes a network of hydrogen bonds to the hydroperoxido ligand. Systematic deletions of individual hydrogen bonds to the Cu-OOH complex were accomplished using different Sav variants and demonstrated that stability is achieved with a single hydrogen bond to the proximal O-atom of the hydroperoxido ligand: changing this interaction to only include the distal O-atom produced a reactive variant that oxidized an external substrate.

The hydrogen-bonded complexes of the 5-fluorouracil with the DNA purine bases: a comprehensive quantum chemical study

In this research work, various hydrogen-bonded complexes of 5-fluorouracil (FU), as a simplest organic anticancer drug, with the adenine and guanine purine bases were investigated. First, the molecular electrostatic potentials (MEP) of all monomers (FU, A, and G) are explored and their active sites for hydrogen-bonded interactions identified. Then, the selected plausible coplanar complexes were optimized and their complexation energies obtained. Our results reveal that the FU-G complexes are more stable than the FU-A ones. Also, the most stable structures of both series were recognized, which is consistent with the MEP results of monomers. Additionally, we estimated the strengths of the individual hydrogen bonds of the benchmark systems by energetic, geometric, spectroscopic, topological, and molecular orbital descriptors. The acceptable linear correlations between the complexation energies and some of the mentioned descriptors are observed. Finally, several aromatic indices (HOMA, ATI, NICS (0), and NICS (1)) were applied to evaluate the significant of π-electron delocalization (π-ED) of 5/6 membered rings. These results show that the π-ED of the benchmark systems increases with the formation or strengthening of the HB, which is in line with the resonance-assisted hydrogen bond theory.

Characterization of Individual Hydrogen Bonds in Crystalline Regenerated Cellulose Using Resolved Polarized FTIR Spectra.

Cellulose nanofibers (CNFs), which are directly isolated as a native form, have drawn considerable attention as eco-friendly and distinctive material to be partly substituted for fossil products. In addition to the increasing attention to the native CNFs, conventional regenerated cellulose having cellulose II crystals also attracts more attention because of its cost-effective method of production in a moderately easy and repeatable fashion. Inter- and intramolecular hydrogen bonds are, in particular, thought to contribute greatly to the physical properties of cellulosic commercial products. More than half century ago, Marchessault et al. attempted to directly assign the hydroxyl (OH) group vibrations related to hydrogen bonding in infrared (IR) spectra. The assignment, however, has not been significantly updated. One reason for the delayed assignments is the difficulty in preparing pure cellulose II. Here, we show successful IR assignments of the interacted OH groups in cellulose II by using the nematic ordered cellulose to prepare a highly oriented regenerated film. The film had anisotropic crystalline domains, which provided a clearly resolved component in the IR spectra. The OH bands were well assigned, and this IR assignment becomes an effective tool to understand the structure–property relationship for engineering advanced regenerated cellulose materials.

Nuclear quantum effects of hydrogen bonds probed by tip-enhanced inelastic electron tunneling.

We report the quantitative assessment of nuclear quantum effects on the strength of a single hydrogen bond formed at a water-salt interface, using tip-enhanced inelastic electron tunneling spectroscopy based on a scanning tunneling microscope. The inelastic scattering cross section was resonantly enhanced by "gating" the frontier orbitals of water via a chlorine-terminated tip, so the hydrogen-bonding strength can be determined with high accuracy from the red shift in the oxygen-hydrogen stretching frequency of water. Isotopic substitution experiments combined with quantum simulations reveal that the anharmonic quantum fluctuations of hydrogen nuclei weaken the weak hydrogen bonds and strengthen the relatively strong ones. However, this trend can be completely reversed when a hydrogen bond is strongly coupled to the polar atomic sites of the surface.