Red-shifted Hydrogen Bonds Research Articles

Insight into structure, stability and hydrogen bond in complexes of guanine and thymine at the molecular level using computational chemical method

Nine stable structures of complexes formed by interaction of guanine with thymine were located on potential energy surface at B3LYP/6-311++G(2d,2p). The complexes are quite stable with interaction energy from -5,8 to -17,7 kcal.mol-1. Strength of complexes are contributed by hydrogen bonds, in which a pivotal role of N−H×××O/N overcoming C−H×××O/N hydrogen bond, up to to 3.5 times, determines stabilization of complexes investigated. It is found that polarity of N/C−H covalent bond over proton affinity of N/O site governs stability of hydrogen bond in the complexes. The obtained results show that the N/C−H×××O/N red-shifting hydrogen bonds occur in all complexes, and a larger magnitude of an elongation of N−H compared C-H bond length accompanied by a decrease of its stretching frequency is detected in the N/C−H×××O/N hydrogen bond upon complexation. The SAPT2+ analysis indicates the substantial contribution of attractive electrostatic energy versus the induction and dispersion terms in stabilizing the complexes.

Structural and spectral properties of astronomical complex organic molecules: 1:1:1 glycine-X-Y and Y-glycine-X

Current research to understand astrochemistry and astrobiology with regard to the weakly bound astronomical complexes including amino acids in the Inter-Stellar Medium (ISM), comets and meteorites at molecular level are flourishing and many new findings are emerging rapidly. Modern experimental techniques and computational investigations assisted by quantum chemical analysis are playing key role towards exploring the evolution of many molecular complexes in astrochemical environment and planetary atmospheres by affecting their stability as well as their structural and spectral properties. The present work deals with weekly bound complexes of glycine with small molecules like water, ammonia and HF as 1:1:1 Glycine-X-Y and Y-Glycine-X. The affects that influence the complexation, mainly involve through non-covalent interactions with these small molecules have been explored, based on various properties of the red shifted hydrogen bonds of the type: OHO, NHO, FHO, OHN and carbon-cantered blue shifted hydrogen bonds, CHO type, for all the stable complexes of 1:1:1 Glycine-X-Y and Y-Glycine-X with respect to their structural properties and spectral characterization. The computed Ray's asymmetry parameter, κ values for the investigated 1:1:1 Glycine-X-Y and Y-Glycine-X complexes are found to be negative and predicted as prolate-type asymmetric rotor. The computed rotational constants and IR spectra of these different complexes may assist in the interpretation and analysis of observational data and the data obtained in laboratory experiments. The possibilities of formation of such molecular complexes in the interstellar space may provide a direction to explore new possibilities.

An ab initio study of some hydrogen-bonded complexes of chloroform and bromoform: red-shifted or blue-shifted hydrogen bonds?

The properties of the hydrogen-bonded complexes of chloroform and bromoform with ammonia, water, hydrogen fluoride, phosphine, hydrogen sulphide and hydrogen chloride were studied by means of ab initio calculations. The properties of interest were the molecular structures, the interaction energies, the vibrational spectra and the nature of the orbital interactions involved in the formation of the complexes. Of particular interest was the determination of whether the various interactions exhibited red-shifted or blue-shifted hydrogen bond behaviour. The complexes optimized in three distinct structural models, singly bonded, cyclic and cage. The interaction energies, in the main, varied systematically with changes of the haloform and of the partner molecules. Changes of the CH or YH (Y = N, O, F, P, S and Cl) bond lengths correlated in most cases with the interaction energies, subject to some inconsistencies, with opposite behaviour being shown by the two sets. Similarly, the CH and YH stretching wavenumber shifts also displayed a dependence on the interaction energies, tracking with the bond length changes. Based on the diagnostic utility of these structural and spectroscopic properties, the complexes were found to be almost exclusively red-shifted, for binding through both the CH and YH groups. The orbital interactions responsible for the stability of the complexes were determined to be donation from a Y atom lone pair orbital of the partner molecule to a CH σ antibonding orbital and from a X lone pair orbital (X = Cl and Br) of the haloform to a YH σ antibonding orbital.

Electronic-level insight into the weak interactions of ion pairs in acetate anion-based ionic liquids

The weak interactions in ion pairs of acetate anion-based ionic liquids (ILs) were investigated by dispersion-corrected density functional theory (DFT) calculations, where the structural parameters and vibrational frequency changes of ion pairs and isolated ions were systematically analyzed. Four kinds of stable configurations for ILs 1-ethyl-3-methylimidazolium acetate ([Emim][OAc]) and 1-butyl-3-methylimidazolium acetate ([Bmim][OAc]) were determined by calculating the interaction energies of different ion pairs. The essence of weak interactions between ion pairs was qualitatively and quantitatively characterized by the electrostatic potential (ESP) of anions and cations, natural bond orbital (NBO), atoms in molecules (AIM), and Generalized Kohn-Sham energy decomposition analysis (GKS-EDA). The results indicated that the red-shifted hydrogen bond (H-bond) of C1-H2⋯O contributed the most to the stability of ion pairs. For the different stable ion pairs, the H-bond interactions formed by acetate anion ([OAc]−) with H protons on the imidazolium ring and side chain were separately divided into medium and weak H-bond, showing partly covalent and noncovalent nature. GKS-EDA results revealed that the interactions of ion pairs were mainly electrostatic dominant, charge transfer and orbital overlap contributions were also significant, which were in accordance with the ESP, NBO, and AIM analyses results. Hopefully, this study could offer an insight into weak interactions principle of ILs and provide a theoretical basis for predicting their physicochemical properties.

Experimental and theoretical studies on the bifurcated hydrogen bonded NLO active material of pure and crystal violet dye-doped L-argininium bis dihydrogen phosphate

Single crystals of pure and crystal violet dye-doped L-Argininium bis dihydrogen phosphate were grown using slow evaporation technique. The crystalline nature and the structure parameters were confirmed by powder X-ray diffraction technique. Blue and red shifting hydrogen bonds were predicted by DFT on the basis of vibrational spectral (FT-IR & FT-Raman), AIM and NBO analyses. Bifurcated NH⋯O and OH⋯O intermolecular hydrogen bonds in LADP molecule were visualized by Hirshfeld surface. 13C and 1H NMR spectroscopy confirmed the structure of LADP. Doped LADP crystal shows enhancements in the wavelength and longer lifetimes as identified from photoluminescence spectra and decay analysis respectively. The high values of electron mobility and low value of λelectron reflect the applicability of LADP in OLED devices. Enhancement in nonlinear optical parameters in dye-doped LADP crystal was revealed from the Z-scan technique which shows its usefulness in the fabrication of NLO devices.

Characterization of blue-shifting hydrogen bonds in small complexes

ABSTRACTThe so-called improper blue-shifting (BS) Hydrogen bond, characterising some small complexes, is theoretically investigated by first-principles calculations based on the Density Functional Theory. We compute structural, energetic, electronic and electrostatic properties not only of complexes with linear Hydrogen bonds but also of systems with multiple intermolecular contacts leading to the formation of ‘bifurcated’ or even ‘trifurcated’ Hydrogen bonds. In particular, Hydrogen bonds are characterised in terms of differential electron densities distributions and profiles, and of the shifts of the centres of Maximally localised Wannier Functions. The information from the latter quantities can be conveyed into simple geometric bonding parameters that are helpful in characterising the interatomic bonds. The effect of including dispersion corrections for describing BS Hydrogen bonds is also investigated. Our detailed comparison of the properties of systems with BS Hydrogen bonds to those of others, where more conventional red-shifting Hydrogen bonds are formed, supports the view that there is no fundamental difference between the two kinds of bonds.

An ab initio study of some binary complexes containing methyl fluoride and difluoromethane: red-shifting and blue-shifting hydrogen bonds

ABSTRACTThe properties of a number of hydrogen-bonded complexes of methyl fluoride and difluoromethane with a range of hydrides of the first two rows of the periodic table have been computed using ab initio molecular orbital theory. The aim of this work was to identify possible examples of blue-shifting hydrogen-bonded species analogous to those formed between fluoroform and ammonia, water, phosphine and hydrogen sulphide, reported earlier. The calculations were carried out using the Gaussian-09 program, at the second-order level of Møller–Plesset perturbation theory, and with the aug-cc-pVTZ basis sets of Dunning. The properties studied include the molecular structures, the hydrogen bond energies and the vibrational spectra. The results have been interpreted with the aid of natural bond orbital theory and the quantum theory of atoms in molecules.

Quantitative relationships between bond lengths, stretching vibrational frequencies, bond force constants, and bond orders in the hydrogen-bonded complexes involving hydrogen halides

To uncover the correlation between the bond length change and the corresponding stretching frequency shift of the proton donor D–H upon hydrogen bond formation, a series of hydrogen-bonded complexes involving HF and HCl which exhibit the characteristics of red-shifted hydrogen bond were investigated at the MP2/aug-cc-pVTZ, M062X/aug-cc-pVTZ, and B3LYP/aug-cc-pVTZ(GD3) levels of theory with CP optimizations. A statistical analysis of these complexes leads to the quantitative illustrations of the relations between bond length and stretching vibrational frequency, between bond length and bond force constant, between stretching vibrational frequency and bond force constant, between bond length and bond order for hydrohalides in a mathematical way, which would provide valuable insights into the explanation of the geometrical and spectroscopic behaviors during hydrogen bond formation.

Effect of electron-donating and electron-withdrawing atoms on the C–H…Y hydrogen bond in model X3CH…YZ (X = B, F; YZ = BF, CO, N2) complexes

ABSTRACTA computational study of model complexes X3CH…YZ (X = B, F; YZ = BF, CO, N2) was undertaken to assess the effect of electron-donating and electron-withdrawing X atoms on the properties of the C–H…Y hydrogen bond. Sequential substitution of the B atoms in B3CH by F atoms to produce F3CH allowed for the elucidation of interesting trends in the corresponding hydrogen-bonded complexes. The dipole moments and the dipole moment derivative with respect to C–H bond displacement for the proton donors and the chemical hardness of the Y atom of the proton acceptor YZ were found to be useful parameters for understanding these trends. It was found that a positive dipole derivative favours red-shifted hydrogen bonds, whereas a negative dipole derivative favours blue-shifted hydrogen bonds. However, decreasing hardness of Y (which correlates with increasing intermolecular attraction) modifies the interaction such that either greater C–H bond extensions/red shifts or smaller C–H bond compressions/blue shifts are obtained.

Double hydrogen bond interaction in 7-azaindole complexes with protic solvents

The double hydrogen bond interaction between 7-azaindole (7AI) and protic solvents including methanol (MeOH), formamide (FM), formic acid (FA), pyridone (PY) and 7AI has been investigated as a proper model of mutations generated by tautomeric shifts in hydrogen-bonded bases of DNA. The results confirm electrostatic nature for all considered hydrogen bonds except for NH hydrogen bond in 7AI-FA. The largest interaction and polarization energies are obtained for 7AI-FA by means of energy decomposition analyses (EDA). The EDA results show an inverse competitive correlation between polarization and electrostatic components of attraction energy to determine the nature of hydrogen bond. The red-shifted hydrogen bonds are identified for all complexes as a result of hyperconjugation, except for 7AI-MeOH, which its blue-shift effect is attributed to the rehybridization dominating of CH bond. Investigation of aromaticity indices for 7AI complexes represents an increase in aromaticity of pentagonal ring and a decrease in hexagonal ring. Finally, the double hydrogen bond between 7AI and FA is identified as dominant interaction to achieve the tautomerization of 7AI in all applied approaches.

Study of molecular interaction in the mixtures of benzene + methyl acrylate/butyl acrylate through dielectric and spectroscopic studies

Binary mixtures of benzene+methyl acrylate/butyl acrylate were prepared over the entire composition range which were subjected to dielectric and spectroscopic (FTIR, 13C NMR and UV–vis) studies. The parameters such as Kirkwood correlation factor, excess dielectric constant etc. are interpreted with the aid of spectroscopic results which revealed the existence of blue and red shifting hydrogen bonds in both the mixtures. 13C NMR and excess free energy ∆G favor the presence of self-associated molecular aggregates in neat methyl acrylate/butyl acrylate.

On the Nature of Blueshifting Hydrogen Bonds

The block-localized wave function (BLW) method can derive the energetic, geometrical, and spectral changes with the deactivation of electron delocalization, and thus provide a unique way to elucidate the origin of improper, blueshifting hydrogen bonds versus proper, redshifting hydrogen bonds. A detailed analysis of the interactions of F(3)CH with NH(3) and OH(2) shows that blueshifting is a long-range phenomenon. Since among the various energy components contributing to hydrogen bonds, only the electrostatic interaction has long-range characteristics, we conclude that the contraction and blueshifting of a hydrogen bond is largely caused by electrostatic interactions. On the other hand, lengthening and redshifting is primarily due to the short-range n(Y)→σ*(X-H) hyperconjugation. The competition between these two opposing factors determines the final frequency change direction, for example, redshifting in F(3)CH⋅⋅⋅NH(3) and blueshifting in F(3)CH⋅⋅⋅OH(2). This mechanism works well in the series F(n)Cl(3)-n CH⋅⋅⋅Y (n=0-3, Y=NH(3), OH(2), SH(2)) and other systems. One exception is the complex of water and benzene. We observe the lengthening and redshifting of the O-H bond of water even with the electron transfer between benzene and water completely quenched. A distance-dependent analysis for this system reveals that the long-range electrostatic interaction is again responsible for the initial lengthening and redshifting.

키랄(S)-이부푸로펜 함유 고분자의 합성과 제조된 고분자의 분자 인식 메카니즘

A group of molecularly imprinted polymers (MIPs) with specific recognition for chiral (S)-ibuprofen were successfully prepared based on hydrogen bonds, utilizing <TEX>${\alpha}$</TEX>-methacrylic acid as a functional monomer. The IR analysis of MIPs showed that the blue- and red-shifted hydrogen bonds were formed between templates and functional monomers in the process of self-assembly imprinting and re-recognition, respectively. According to UV-Vis analysis, we found that the ratio of host-guest complexes between template molecule and functional monomer was 1:1. The effect of cross-linker's quantity on the polymerization was studied by transmission electron microscope (TEM). The adsorption selectivity experiments indicated that MIPs exhibited higher selectivity to (S)-ibuprofen than those to ketoprofen and (R)-ibuprofen, (S)-ibuprofen's structural analogs.

A theoretical study on the red- and blue-shift hydrogen bonds of cis-trans formic acid dimer in excited states

Abstract The excited states of cis-trans formic acid dimer and its monomers have been investigated by time-dependent density functional theory (TDDFT) method. The formation of intermolecular hydrogen bonds O1-H1...O2=C2 and C2-H2...O4=C1 induces bond length lengthening of the groups related to the hydrogen bond, while that of the C2-H2 group is shortened. It is demonstrated that the red-shift hydrogen bond O1-H1...O2=C2 and blue-shift hydrogen bond C2-H2...O4=C1 are both weakened when excited to the S1 state. Moreover, it is found that the groups related to the formation of red-shift hydrogen bond O1-H1...O2=C2 are both strengthened in the S1 state, while the groups related to the blue-shift hydrogen bond C2-H2...O4=C1 are both weakened. This will provide information for the photochemistry and photophysical study of red- and blue-shift hydrogen bond.

Matrix-isolation infrared studies of 1:1 molecular complexes containing chloroform (CHCl3) and Lewis bases: Seamless transition from blue-shifted to red-shifted hydrogen bonds

The infrared spectra of molecular complexes containing chloroform (CHCl(3)) and Lewis bases (N(2), CO, H(2)O, and CH(3)CN) have been observed in an Ar matrix, and vibrational peaks for the 1:1 complexes have been assigned. The C-H stretching band of chloroform in the complexes showed a seamless transition from a blue shift (for N(2) and CO) to a red shift (H(2)O and CH(3)CN), in accord with the proton affinity of the base molecules. Density functional calculations predicted that the C-H··(σ-type lone pair) isomer is the most stable, which is consistent with the observed vibrational peak shift upon complex formation. The underlying mechanisms of the C-H hydrogen bond were explored using the topological properties of the electronic charge density and natural orbital analyses.

Blue and red shift hydrogen bonds in crystalline cobaltocinium complexes

Typical hydrogen-bonded cobaltocinium salts of formula [Cp2Co+][A−] [with Cp = C5H5 and A = PF6 ( 1), AsF6 ( 2), SbF6 ( 3), I ( 4), I3 ( 5), Co(CN)6 ( 6), Co(CO)4 ( 7), Br3 ( 8), FeI4 ( 9) and HCl2 ( 10)] were studied by means of a combined structural, spectroscopic (IR, Raman, solid-state NMR) and theoretical approach. The solid-state vibrational spectra show blue or red shift hydrogen bond behavior depending on the anionic species, i.e. high- or low-frequency ν(CH) shift with respect to the solution value. The crystal structure of the new complex [Cp2Co+][SbF6−], a blue-shifted system, is reported while the [Cp2Co+][I−] complex, a red-shifted system disordered at room temperature, reveals a novel ordered polymorph at 150 K. The weak interactions (C⋯H, H⋯H, H⋯X, C⋯X) between cations and anions were analyzed by means of the Hirshfeld surfaces model, which permits their clear graphic visualization. HS fingerprint plots and normalized contact distances visually describe the difference between blue- and red-shifted complexes. Chemical shift tensors and shielding anisotropy values of the Cp carbon atoms, extracted from 13C CPMAS solid-state NMR spectra, allow the evaluation of Cp rotational motions which are related to the intermolecular contact extent. Finally, a DFT computational model is able to rationalize all the experimental data. It shows that the prevalence of one between two forces, that is, the attractive polarization of C–H bonds and the repulsive effect of electronic clouds, leads to the blue or red shift phenomenon.

Theoretical Study of [Ni (H2O)n]2+(H2O)m (n ≤ 6, m ≤ 18)

The [Ni-(H(2)O)(n)](2+)(H(2)O)(m) (n ≤ 6, m ≤ 18) complexes were studied by means of first-principles all-electron calculations performed with the BPW91 gradient corrected functional and the 6-311+G(d,p) basis sets for the H, O, and Ni atoms. Triplet states were found as low-lying states for each (n, m) combination. The estimated Ni(2+)-(H(2)O)(n) binding energies (112.8-57.4 kcal/mol for the first layer and 52.0-23.0 kcal/mol for the second one) decreases and the Ni(2+)-OH(2) bond lengths lengthen as n + m increases. With six H(2)O moieties the Ni(2+) ion furnishes its first coordination sphere of octahedral geometry. Further water addition renders the formation of the second layer. The effect of Ni(2+) on the (H(2)O)(n)···(H(2)O)(m) hydrogen bond formation for several "n" and "m" combinations was studied, revealing an enhancement of this kind of bonding, which is of key importance for the stabilization and growth of the clusters. For some n + m isomers the second layer appears before the first octahedral layer is fully formed. For example, the square planar Ni(2+)-(H(2)O)(4) core originates two-dimensional 4 + 2 and 4 + 4 isomers, where each outer water molecule accepts two H-bonds, lying 2.0 kcal/mol above the 6 and 6 + 2 ground states. The clusters were also studied by IR spectra; the OH stretching vibrational frequencies allowed us to identify the outer solvation shells by the presence of red-shifted hydrogen bond regions.

First-principles study of fluoroform adsorption on a hexagonal ice (0001) surface: weak hydrogen bonds—strong structural effects

For isolated fluoroform (F(3)CH) molecules adsorbed on a hexagonal ice (0001) surface the properties of blue- and red-shifting hydrogen bonds were studied using static density functional theory (DFT) calculations and Car-Parrinello molecular dynamics (CP-MD) simulations. A systematic search by starting from many initial configurations was performed to determine the lowest-energy structures of F(3)CH on the ice surface, and for the optimized geometries the vibrational frequencies were calculated. The local minima structures are analyzed in terms of their coordination to the surface, with special focus on identifying blue-shifting hydrogen bonds via their spectroscopic signature of an increased frequency of the C-H fundamental stretching vibration. Subsequently, by CP-MD simulations the stability of the lowest-energy configurations at finite temperatures was verified and possible transformation pathways connecting the local minima structures were explored.

Halogen as halogen-bonding donor and hydrogen-bonding acceptor simultaneously in ring-shaped H3N·X(Y)·HF (X = Cl, Br and Y = F, Cl, Br) Complexes

A series of ring-shaped molecular complexes formed by H(3)N, HF and XY (X = Cl, Br and Y = F, Cl, Br) have been investigated at the MP2/aug-cc-pVTZ level of theory. Their optimized geometry, stretching mode, and interaction energy have been obtained. We found that each complex possesses two red-shifted hydrogen bonds and one red-shifted halogen bond, and the two hydrogen bonds exhibit strong cooperative effects on the halogen bond. The cooperativity among the NH(3)···FH, FH···XY and H(3)N···XY interactions leads to the formations of these complexes. The AIM analysis has been performed at the CCSD(T)/aug-cc-pVQZ level of theory to examine the topological characteristics at the bond critical point and at the ring critical point, confirming the coexistence of the two hydrogen bonds and one halogen bond for each complex. The NBO analysis carried out at the B3LYP/aug-cc-pVTZ level of theory demonstrates the effects of hyperconjugation, hybridization, and polarization coming into play during the hydrogen and halogen bonding formations processes, based on which a clockwise loop of charge transfer was discovered. The molecular electrostatic potential has been employed to explore the formation mechanisms of these molecular complexes.

Ab initio studies of the vibrational spectra of some hydrogen-bonded complexes of fluoroacetylene

Ab initio molecular orbital theory has been used to compute the properties of a number of hydrogen-bonded complexes between fluoroacetylene as proton donor and ammonia, water, hydrogen fluoride, phosphine, hydrogen sulfide, and hydrogen chloride as proton acceptors. The properties considered were the vibrational spectra, the molecular structures, the hydrogen-bond energies, and the electron densities, and one of the aims of the study was to ascertain whether there was any evidence of blue-shifting hydrogen-bond character in the complexes formed. The adducts with NH3, H2O, PH3, and H2S were of the conventional CH···X kind (X = N, O, P, S), with hydrogen-bond energies decreasing in the order NH3 &gt; H2O &gt; PH3≈ H2S. Those formed with HF and HCl showed the presence of three alternative structures; in addition to the CH···F(Cl) complexes, adducts of the F(Cl)H···F and F(Cl)H···π type were also found to be stationary points on the potential energy surfaces, with stabilities in the order F(Cl)H···π &gt; CH···F(Cl) &gt; F(Cl)H···F. The hydrogen-bond energies of the CH···X series correlated with the gas-phase basicities of the proton acceptors; moreover, the CH bond-length changes, the wavenumber shifts, the complex–monomer infrared intensity ratios of the CH stretching modes, and the amounts of charge transferred on complex formation were all found to track with the hydrogen-bond energies. All those properties considered here are consistent with the formation of red-shifting hydrogen bonds, to the exclusion of the blue-shifting alternatives.