The effect of benzo‐annelation on intermolecular hydrogen bond and proton transfer of 2‐methyl‐3‐hydroxy‐4(1H)‐quinolone in methanol: A TD‐DFT study

Excited‐state intermolecular or intramolecular proton transfer (ESIPT) reaction has important potential applications in biological probes. In this paper, the effect of benzo‐annelation on intermolecular hydrogen bond and proton transfer reaction of the 2‐methyl‐3‐hydroxy‐4(1H)‐quinolone (MQ) dye in methanol solvent is investigated by the density functional theory and time‐dependent density functional theory approaches. Both the primary structure parameters and infrared vibrational spectra analysis of MQ and its benzo‐analogue 2‐methyl‐3‐hydroxy‐4(1H)‐benzo‐quinolone (MBQ) show that the intermolecular hydrogen bond O₁―H₂?O₃ significantly strengthens in the excited state, whereas another intermolecular hydrogen bond O₃―H₄?O₅ weakens slightly. Simulated electron absorption and fluorescence spectra are agreement with the experimental data. The noncovalent interaction analysis displays that the intermolecular hydrogen bonds of MQ are obviously stronger than that of MBQ. Additionally, the energy profile analysis via the proton transfer reaction pathway illustrates that the ESIPT reaction of MBQ is relatively harder than that of MQ. Therefore, the effect of benzo‐annelation of the MQ dye weakens the intermolecular hydrogen bond and relatively inhibits the proton transfer reaction.     

The role of water in the design of glycosidic linkage flexibility

In this paper we show how a variety of computational methods are used to understand the role that water plays in the solution conformational dynamics of carbohydrates. A comparison is made between maltose and a designed disaccharide (α-D-Glc-NAc-(1→4)-β-D-Glc-3-NH₂) in which the cross glycosidic linkage hydrogen bonds have been significantly strengthened. However, despite the stronger intramolecular hydrogen bonds in the maltose derivative, the correlation times for glycosidic dihedral angle fluctuations are approximately the same for the two sugars. Upon investigation of the water in the first hydration shells for the two disaccharides, high water probability densities were found between the functional groups straddling the glycosidic linkage that bonds the two monosaccharides together. This probability density corresponds to single water molecules forming bridging hydrogen bonds between the functional groups on either side of the linkage for periods of 3.66 ps in the case of maltose and 8.36 ps in the case of the amine derivative. Ab initio studies of saccharide structure interaction with single water molecules reveal that these intermolecular (sugar-solvent) hydrogen bonds are of similar strength to the intramolecular (sugar-sugar) hydrogen bonds. This combination of molecular dynamics and ab initio computational methods demonstrates that increasing the internal hydrogen bond strength in oligosaccharides does not lead to significantly slower internal molecular motion of these sugars in solution. The intermolecular hydrogen bonds formed with water compete equally with the intramolecular hydrogen bonds in the sugar. This result has important implications when considering hydrophobic versus hydrophilic effects in glycoproteins.     

Intra‐ and intermolecular N?H···O hydrogen bonds in pyrrolyl derivatives of indane‐1,3‐dione – experimental and theoretical study

2‐(Pyrrol‐2‐ylmethylene)‐1,3‐indandione ( 4 ) and 2‐(pyrrol‐2‐ylmethylene)‐3‐dicyanomethylidene‐1‐indanone ( 5 ) were synthesized. Multinuclear and 2D‐NMR, IR, UV spectroscopic investigations as well as quantum chemical calculations showed the presence of strong hydrogen bonding in these molecules. For both molecules, the presence of two conformers, with and without H‐bond, was experimentally detected in the basic solvents (DMSO, acetone, pyridine) and the solvate complexes were theoretically calculated. Specific behavior of the intramolecular H‐bonded complexes different from that of the intermolecular H‐complexes is discussed. Copyright © 2009 John Wiley & Sons, Ltd.     

Acid‐base properties and supramolecular structure of N‐[(hydroxymethyl)triazolyl]triflamides: DFT,ab initio,and FTIR study

For N‐{[2‐(hydroxymethyl)‐2H‐1,2,3‐triazolyl‐4‐yl]methyl}triflamide 1 , N‐{[2‐(hydroxymethyl)‐2H‐1,2,3‐triazolyl‐4‐yl]methyl}‐N‐phenyltriflamide 2 , and N,N‐bis{[2‐(hydroxymethyl)‐2H‐1,2,3‐triazolyl‐4‐yl]methyl}triflamide 3 , the proton affinities of the triazole nitrogen atoms and the hydroxy and sulfonyl oxygen atoms as well as the energies of formation of the conformers with intramolecular H‐bonds and dimers with intermolecular NH?N, OH?N, OH?O═S, and NH?O═S H‐bonds were calculated by density functional theory and second‐order Møller‐Plesset perturbation methods. Quantum Theory of Atoms in Molecules analysis was performed to investigate the nature of H‐bonds. According to Fourier transform infrared spectroscopy, in CH₂Cl₂ solution, the monomeric molecules of 1 to 3 exist in the equilibrium with cyclic dimers having the OH?N hydrogen bonds.     

Intra‐ versus intermolecular hydrogen bonding equilibrium in 2‐hydroxy‐N,N‐diethylbenzamide

Complex studies of the intramolecular versus intermolecular hydrogen bond equilibrium and internal rotation of the N,N‐diethylamine group in 2‐hydroxy‐N,N‐diethylbenzamide were conducted. The intramolecular versus intermolecular process in 2‐hydroxy‐N,N‐diethylbenzamide was studied by UV–Vis, NMR, IR and Vapour Pressure Osmometric (VPO) methods as a function of temperature and concentration in non‐polar, basic and protic solvents. The unequal positions of the ethyl groups were analysed and the energy barrier to the re‐orientation was defined by the NMR method. This paper presents a study into a complicated nature of competitive interaction 2‐hydroxy‐N,N‐diethylbenzamide with the environment by means of the aforesaid methods. Copyright © 2008 John Wiley & Sons, Ltd.     

On the structure of 3‐acetylamino‐5‐methyl‐1,2,4‐oxadiazole and on the fully degenerate rearrangements (FDR) of its anion: a stimulating comparison between the results of ‘in‐silicon chemistry’ and ‘laboratory chemistry’

An accurate crystal structure determination has provided evidence for a planar conformation for 3‐acetylamino‐5‐methyl‐1,2,4‐oxadiazole ( 5 ), in agreement with quantum‐mechanical calculations in the gas phase. In the crystal, a series of strong intermolecular N7H7^….O9 hydrogen bonds link the amido groups of different molecules, causing the formation of infinite parallel ordered chains. The effect of the DMSO solvent on the energy and charge distribution of compound 5 and on its relevant 5 ^? anion, involved in a fully degenerate rearrangement (FDR), has been deepened by quantum‐mechanical DFT calculations. The calculated energy barrier for the FDR increases in going from in vacuo to DMSO, in agreement with previsions based on the Hughes and Ingold rules concerning the nucleophilic substitution of an anionic reagent (the deprotonated amido group in the side chain) on a neutral substrate (the 1,2,4‐oxadiazole ring). Copyright © 2009 John Wiley & Sons, Ltd.     

Antioxidant phenolic esters with potential anticancer activity: solution equilibria studied by Raman spectroscopy

The solution Raman pattern of a series of structurally related hydroxycinnamic and hydroxybenzoicesters (caffeates and gallates) with potential antioxidant/anticancer activity was studied, for different biologically significant concentrations. The spectra were assigned with the help of theoretical calculations in the light of previously reported experimental data for these compounds in the solid state. Evidence of the formation of dimeric entities in solution, via (C)···O···H(O) and/or (C)O···H(C) intermolecular hydrogen bonds, was obtained. The dimer‐to‐monomer equilibrium, which influences the antioxidant activity of this kind of systems, was monitored through Raman titration experiments. Copyright © 2008 John Wiley & Sons, Ltd.     

Excited‐state hydrogen bonding dynamics of pyruvic acid and geminal‐diol, 2,2‐dihydroxypropanoic acid in aqueous solution: a DFT/TDDFT study

In this work, we present the optimized ground state geometrical structures, electronic excitation energies and corresponding oscillation strengths of the low‐lying electronically excited states for the isolated Tce‐CH3COCOOH and Tce‐CH3C(OH)2COOH as well as their corresponding hydrogen‐bonded dimers Tce‐CH3COCOOH‐H2O and Tce‐CH3C(OH)2COOH‐H2O through time‐dependent density functional theory method. It is found that the intermolecular hydrogen bonds C=O···H‐O are strengthened in the electronically excited states of the hydrogen‐bonded dimers Tce‐CH3COCOOH‐H2O and Tce‐CH3C(OH)2COOH‐H2O, in that the excitation energies of the related excited states for the hydrogen‐bonded dimers are decreased compared with those of the corresponding monomers. The calculated results are consistent with the rules that are first demonstrated by Zhao on the excited‐state hydrogen bonding dynamics. Copyright © 2012 John Wiley & Sons, Ltd.     

Structure and vibrational analysis of 1‐hydroxy naphthalene based on density functional theory calculations

The solid phase mid‐FTIR and FT‐Raman spectra of 1‐hydroxy naphthalene (HNP) were recorded in the regions 4000–400 and 4000–50 cm, respectively. The spectra were interpreted with the help of normal coordinate analysis following full structure optimization and force field calculations based on the density functional theory (DFT) using the standard B3LYP/6‐31G** method and basis set combination. The results of the calculations were applied to simulate infrared and Raman spectra of the title compound which showed excellent agreement with the observed spectra. Copyright © 2009 John Wiley & Sons, Ltd.     

Hydrogen bonding in liquid water: An ab initio QM/MM MD simulation study

Pattern and dynamics of hydrogen bonds in liquid water were investigated by a quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulation at Hartree–Fock (HF) level of theory. A large subregion of the whole system comprising two complete coordination shells was treated quantum mechanically in order to include all polarization and charge transfer effects and to obtain accurate data about structure and dynamics of the intermolecular bonds. The results of this investigation are in agreement with recent experimental findings and suggest that in liquid water every molecule forms in average 2.8, but almost as a rule less than four intermolecular hydrogen bonds.     

Intramolecular and intermolecular hydrogen bonds in aminophenols

IR-Fourier spectroscopy methods are adopted to study intramolecular and intermolecular hydrogen bonds that form in CCl₄ solutions of aminophenol derivatives and in a solid phase of these compounds pressed in KBr. If a hydroxyl group is present in the molecule in the ortho-position to an amino group, then intramolecular interactions between OH and NH groups will take place in aminophenol solutions. Intramolecular O–H⋅⋅⋅O=S=O and N–H⋅⋅⋅O=S=O hydrogen bonds are found in solutions of compounds containing a sulfonamide fragment. Additional acylation of the amino group causes an intramolecular O–H⋅⋅⋅O=C hydrogen bond to form in solutions. Functional groups OH, NH, SO₂, and C=O interact with one another in various ways in the solid phase to form intermolecular hydrogen bonds in aminophenols.     

Weak and strong hydrogen bonds conducting the supramolecular framework of 1-butyl-3-(1-naphthoyl)thiourea: crystal structure,vibrational studies,DFT methods,Pixel energies and Hirshfeld surface analysis

A detailed structural and spectroscopic study of a new thiourea derivative 1-butyl-3-(1-naphthoyl)thiourea (1) is presented with the assistance of theoretical calculations. The X-ray diffraction structure analysis reveals a planar carbonylthiourea group, favoured by intra-molecular NH···O bond. The compound is arranged in the lattice as NH···O and NH···S bonded polymeric ribbons, that extend along the crystal b-axis. Molecular pairs involving N–H···S hydrogen bonds are a dominant contribution to packing stabilisation coming from coulombic component. Hirshfeld surfaces and two-dimensional-fingerprint plots show different intermolecular contacts and its relative contributions to total surface in each compound. The AIM approach shows the nature and strength of the strong and weak intramolecular interactions and the solvent effect, while NBO analysis reveals that the sulphur atom is responsible for the higher hyperconjugative stabilising energy.     

Spectroscopic and thermal studies on the inclusion of trans‐cinnamic acid and a number of its hydroxyl‐derivatives with α, β and γ‐cyclodextrins molecules

The inclusion compounds of α‐, β‐ and γ‐cyclodextrins (α‐CD, β‐CD and γ‐CD) with trans‐cinnamic acid (t‐CIA), 3‐hydroxy‐trans‐cinnamic acid (t‐3OHCIA), 4‐hydroxy‐trans‐cinnamic acid (t‐4OHCIA) and 3,4‐dihydroxy‐trans‐cinnamic acid (t‐3,4OHCIA) were prepared and characterized, in the solid state, by means of thermogravimetry and Raman spectroscopy. The effects of the inclusion process on the guest molecules and on the hydrogen bond interactions of the guest were studied by monitoring sensitive vibrational modes, such as CO, CC and ring C H stretching modes. By combining Raman and TG data with ab initio calculations and information from CSD database on similar compounds, inclusion geometries for the different compounds are proposed. The size of the host cavity and the maximization of host/guest hydrogen‐bonding contacts appear to be the main factors determining the inclusion geometries. Copyright © 2009 John Wiley & Sons, Ltd.     

CNDO/2 Calculations for Hydroxy Stretching Bands of Intramolecular Hydrogen Bonds in cis−Cyclohexane-1,3-Diol and cis−3-Aminocyclohexanol

CNDO/2 calculations are used to predict the hydroxy stretching frequency and intensity of the intramolecular hydrogen bonds in the title compounds. The predictions are compared with experimental data.     

On structural and spectroscopic differences between quinoline‐2‐carboxamides and their N‐oxides in the solution and solid state

Intramolecular hydrogen bonding in the primarily and secondarily substituted quinoline‐2‐carboxamides and their N‐oxides has been studied in the solution by multinuclear NMR spectroscopy. Hydrogen bonding patterns and supramolecular arrangement in the solid state have been determined by single crystal X‐ray analysis. In quinoline‐2‐carboxamides weak, nonlinear intramolecular N? H…N hydrogen bond is present, but in the solid state the intermolecular hydrogen bonds and packing forces are the factors that decide on the properties of 3D structures. In quinoline‐2‐carboxamide N‐oxides the most important structural features are the intramolecular hydrogen bonds. Details of different weak interactions and resulting 3D arrangement of molecules are discussed. In the solution, two separate ¹H signals are observed for the primary quinoline‐2‐carboxamides in the range from ca. 5.8 to 8.1 ppm. The chemical shifts of the NH group's proton for studied R′‐quinoline‐2‐R‐carboxamides are in the range from 8.1 to 8.4 ppm. For the N‐oxide of 4‐R′‐quinoline‐2‐carboxamides (R′ = H, Me, OPh, Cl and Br), the values of the proton chemical shifts of the NH group in the range from 10.78 to 11.38 ppm (for primary amides) indicating that this group forms hydrogen bonds with the oxygen of the N‐oxide group. This bond is stronger than the N? H…N bond in quinoline‐2‐carboxamides. For the secondary amide N‐oxides, the δ(NH) values are increasing from 11.25 to 11.77 ppm in the sequence of substituents 4‐Br < 4‐Cl < 4‐H < 4‐Me < 4‐OPh. For 4‐substituted compounds these values depend also on the substituent effect. Copyright © 2009 John Wiley & Sons, Ltd.     

A first-principles study of the structural, electronic and elastic properties of solid nitromethane under pressure

The structural,electronic and elastic properties of solid nitromethane are investigated under pressure by performing first-principles density functional theory(DFT)calculations within the generalized gradient approximation(GGA)and the local density approximation(LDA).The obtained ground state structure properties are found to be consistent with existing experimental and theoretical results.The pressure-induced variations of structure parameters(a,b,c and V)indicate that the solid nitromethane has an anisotropic compressibility,and the compression along the c direction is more difficult than along a and b directions.From the vibration curves of intermolecular bond length and bond angle,we find that the C—N bond is the most sensitive among these bonds under pressure,suggesting that the C—N bonds may be broken first under external loading.The influence of pressure on the electronic properties of solid NM has been studied,indicating that solid NM is an insulating compound with a large indirect band gap and tends to be a semiconductor with increasing pressure.Finally,we predict the elastic constants and their pressure dependence for the solid NM with the bulk modulus,Young’s modulus,shear modulus and the Poisson’s ratio derived.     

NMR and DFT calculation study on structures of 2‐[2‐nitro‐4‐(trifluoromethyl)benzoyl]cyclohexane‐1,3‐dione (NTBC) and its two metabolites isolated from urine of patients suffering from tyrosinemia type I

2‐[2‐Nitro‐4‐(trifluoromethyl)benzoyl]cyclohexane‐1,3‐dione (NTBC) is an active component of nitisinone, a medicine against tyrosinemia type I. Using ¹H, ¹³C and ¹⁹F NMR spectroscopy it has been found that in the urine of patients treated with nitisinone two compounds possessing CF₃ group are always present. They have been isolated by using TLC technique and identified as 4‐hydroxy‐2‐[2‐nitro‐4‐(trifluoromethyl)benzoyl]cyclohexane‐1,3‐dione and 5‐hydroxy‐2‐[2‐nitro‐4‐(trifluoromethyl)benzoyl]cyclohexane‐1,3‐dione, the latter being previously unknown. The constitution, tautomerism and stereochemistry of these compounds have been thoroughly investigated using ¹H and ¹³C NMR spectroscopy supported by theoretical calculations. Molecular structures have been optimized using density functional theory (DFT) with PBE1PBE functional and 6‐31G* basis set. In NMR parameter calculations, the larger 6‐311++G(2d,p) basis set has been used. At both calculation stages, the polarizable continuum model of the solvent has been employed. Copyright © 2010 John Wiley & Sons, Ltd.     

Experimental vibrational spectra (Raman,infrared) and DFT calculations on monomeric and dimeric structures of 2‐ and 6‐bromonicotinic acid

In this work, the Fourier transform infrared and Raman spectra of 2‐bromonicotinic acid and 6‐bromonicotinic acid (abbreviated as 2‐BrNA and 6‐BrNA, C₆H₄BrNO₂) have been recorded in the region 4000–400 and 3500–50 cm⁻¹. The optimum molecular geometry, normal mode wavenumbers, infrared intensities and Raman scattering activities, corresponding vibrational assignments and intermolecular hydrogen bonds were investigated with the help of B3LYP density functional theory (DFT) method using 6‐311++G(d,p) basis set. Reliable vibrational assignments were made on the basis of total energy distribution (TED) calculated with scaled quantum mechanical (SQM) method. From the calculations, the molecules are predicted to exist predominantly as the C1 conformer. Copyright © 2009 John Wiley & Sons, Ltd.