DFT study of the hydrogen bond strength and IR spectra of formic,oxalic, glyoxylic and pyruvic acids in vacuum,acetone and water solution

The molecular geometries of the possible conformations of formic, oxalic, glyoxylic and pyruvic acids have been fully optimized at DFT B3LYP/6‐311++G(d,p) levels of calculation in vacuum as well as in water and acetone solution. Solutions were treated according to the SCRF PCM approach but some formic acid–water and formic acid–acetone clusters as well as adducts of oxalic acid with two or four water molecules were also taken into account for testing the importance of specific solute–solvent effects. All the most stable isomers of the title compounds are characterized by weak intramolecular hydrogen bonds, whose strengths (E_HB) cannot be correctly estimated as stability difference between the open and chelate forms since the energy of the former isomer is, in turn, stabilized by a weak hydrogen bridge due to the formic acid moiety. Following the Rotation Barrier Method (RBM), proposed some years ago, E_HB in the examined molecules (gas phase) falls in the range of 18–22 kJ/mol for oxalic acid (9.6 kJ/mol for the c‐C‐t isomer), 16.8 kJ/mol for glyoxylic acid and 19.8 kJ/mol for pyruvic acid. Most of them disappear at all, or nearly at all, both in acetone and aqueous solution, in consequence of the solvent effect. The frequencies of the OH and C?O stretching modes, calculated according to the anharmonic oscillator model, are in very good agreement with the experimental literature data, where available. Copyright © 2009 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.     

Experimental and computational studies on the solvation of lithium tetrafluorobrate in dimethyl sulfoxide

Solvation structures of the lithium cation and tetrafluorobrate anion in dimethyl sulfoxide (DMSO) were investigated by Raman spectroscopy and ab initio calculations at various salt concentrations. The SO and C S stretching bands were used to monitor the structural change of the solvation shell. It has been shown that the solvation number of Li⁺, calculated by the changes in intensities of the C S asymmetric and symmetric stretching bands, is consistent with the value predicted by ab initio calculations. The wavenumber shift of the C H stretching band is suggested to be the result of the anion solvation and the dissociation of the associated DMSO molecules. Copyright © 2007 John Wiley & Sons, Ltd.     

The structure,dynamics and solvation mechanisms of ions in water from long time molecular dynamics simulations: a case study of CaCl2 (aq) aqueous solutions

Systematic long time (5–20 ns) molecular dynamics (MD) simulations have been carried out to study the structural and dynamical properties of CaCl₂ aqueous solutions over a wide range of concentrations (≤9.26 m) in this study. Our simulations reveal totally different structural characteristics of those yielded from short time (≤1 ns) MD simulations [A.A. Chialvo and J.M. Simonson, J. Chem. Phys. 119, 8052 (2003); T. Megyes, I. Bako, S. Balint, T. Grosz, and T. Radnai, J. Mol. Liq. 129, 63 (2006)]. An apparent discontinuity was found at 4–5 m of CaCl₂ in various properties including ion–water coordination number and self-diffusion coefficient of ions, which were first noticed by Phutela and Pitzer in their thermodynamic modelling [R.C. Phutela and K.S. Pitzer, J. Sol. Chem. 12, 201 (1983)]. In this study, residence time was first taken into consideration in the study of Ca²⁺–Cl^? ion pairing, and it was found that contact ion pair and solvent-sharing ion pair start to form at the CaCl₂(aq) concentrations of about 4.5 and 4 m, respectively, which may be responsible for the apparent discontinuity. In addition, the residence time of water molecules around Ca²⁺ or Cl^? showed that the hydration structures of Ca²⁺ and Cl^? are flexible with short residence time (<1 ns). It needs to be pointed out that it takes much longer simulation time for the CaCl₂–H₂O system to reach equilibrium than what was assumed in previous studies.     

A DFT study of structures of dipicolyl urea isomers and their recognition with carboxylic acids and their carboxylate anions

Four isomers of dipicolyl urea were obtained and the intramolecular hydrogen‐bonded structure was found to be the most stable isomer. Energetics, thermodynamic properties, rate constants, and association constants of their isomerizations computed using the B3LYP/6‐31+G(p,d) method were obtained. Complexes of all isomers of dipicolyl urea with formic acid, acetic acid, benzoic acid, oxalic acid, and their deprotonated species were investigated. Energetics, thermodynamic properties, and rate constants of their associations were obtained. Stabilities of all complexes in terms of association constants of the most stable species were determined. Copyright © 2010 John Wiley & Sons, Ltd.     

Theoretical study on the electronic structures and properties of diindolocarbazole isomers

The objective of this work is to provide an in‐depth interpretation of the electronic structures and optical properties of diindolocarbazole isomers. A systematic study of these different structures caused by the linkage pattern was performed via theoretical calculations. The optimized geometries, electronic properties, frontier molecular orbitals, ionization potentials, electron affinities, reorganization energies, and absorption and emission spectra of these isomers have been calculated and analyzed. Based on the detailed comparisons, the diindolocarbazoles act as candidates of different functional materials for optoelectronic application was predicted and the theoretical reference for the synthesis efforts and experimental investigation was provided. Copyright © 2014 John Wiley & Sons, Ltd.     

Studies on the structures and interactions of glutathione in aqueous solution by molecular dynamics simulations and NMR spectroscopy

All-atom molecular simulations and temperature-dependent NMR have been used to investigate the conformations and hydrogen bonds of glutathione (GSH) in aqueous solution. The simulations start from three different initial conformations. The properties are characterized by intramolecular distances, radius of gyration, root-mean-square deviation, and solvent-accessible surface. GSH is highly flexible in aqueous solutions in the simulations. Moreover, conformations can covert between “extended” and “folded” states. Interestingly, the two different hydrogen atoms in cysteine (H_N2) and glycin (H_N3) show different capabilities in forming NH?OW hydrogen bonds. The temperature-dependent NMR results of the different amide hydrogen atoms also show agreements with the MD simulations. Competing formation of GSH hydrogen-bonding interactions in aqueous solutions leads to hydrogen-bonding networks and the distribution of conformations. These changes will affect the activity of GSH under physiological conditions.     

UV-Raman study and theoretical analogue of picolinic acid in aqueous solution

High quality Raman spectrum of picolinic acid aqueous solution with ultraviolet (UV) excitation of 325 nm was obtained in this article. The state of picolinic acid in aqueous solution has been investigated over a wide range of solution pH values. The distinct changes of UV-Raman spectra accompanied with the pH variations indicate the changes of molecule structure. The calculations based on density functional theory were used to analyze the states of picolinic acid in aqueous solution. By comparing the experimental frequencies with the calculated ones, it can be concluded that when pH value varies from high to low, the picolinic acid tends to change from the anion form to the zwitterion that have the intermolecular hydrogen COOH?N bond.     

Synthesis,tautomeric stability,spectroscopy and computational study of a potential molecular switch of (Z)-4-(phenylamino)pent-3-en-2-one

The (Z)-4-(phenylamino) pent-3-en-2-one (PAPO) was synthesised applying carbon-based solid acid and described by experimental techniques. Calculated results reveal that its keto-amine form is more stable than its enol-imine form. A relaxed potential energy surface scan has been accomplished based on the optimised geometry of NH tautomeric form to depict the potential energy barrier related to intramolecular proton transfer. The spectroscopic results and theoretical calculations demonstrate that the intramolecular hydrogen bonding strength of PAPO is stronger than that in 4-amino-3-penten-2-one)APO(. In addition, molecular electrostatic potential, total and partial density of stats (TDOS, PDOS) and non-linear optical properties of the compound were studied using same theoretical calculations. Our calculations show that the title molecule has the potential to be used as molecular switch.     

Effects of co-solutes on the hydrogen bonding structure and dynamics in aqueous N-methylacetamide solution: a molecular dynamics simulations study

The effects of trimethylamine-N-oxide (TMAO), urea and tetramethyl urea (TMU) on the hydrogen bonding structure and dynamics of aqueous solution of N-methylacetamide (NMA) are investigated by classical molecular dynamics simulations. The modification of the water's hydrogen bonding structure and interactions is calculated in presence of these co-solutes. It is observed that the number of four-hydrogen-bonded water molecules in the solution decreases significantly in the presence of TMAO rather than urea and TMU. The lifetime and structural relaxation time of water–water and NMA–water hydrogen bonds show a strong increase with the addition of TMAO and TMU in the solution, whereas the change is nominal in case of urea solution. It is also found that the translational and rotational dynamics of water and NMA slowdown with increasing the concentration of these osmolytes. The slower dynamics of water and NMA is more pronounced in case of TMAO and TMU solution, as these co-solutes strengthen the average hydrogen bond energies between water–water and NMA–water, whereas urea has a little effect on the hydrogen bonding structure and dynamics of aqueous NMA solution. The calculated self-diffusion coefficient values for water and these co-solutes are in similar pattern with experimental observations.     

Experimental and computational study on the aqueous acidity constants of some new aminobenzoic acid compounds

The acidity constants of three new aminobenzoic acid derivatives were determined using potentiometric and spectrophotometric methods in 0.10 M aqueous potassium nitrate solution as supporting electrolyte. The potentiometric data and UV–Vis absorption spectra of solutions were recorded in the course of their pH-metric titration with a standard base solution. The protolytic equilibrium constants, concentration distribution diagrams and number of components involved have been calculated. The relative pK_a values for three acids were also calculated using ab initio quantum mechanical method at the HF/6-31G** level of theory in combination with CPCM continuum solvation method. The influence of substituents on the ionization constants of the studied molecular structures was investigated. The satisfactory agreement between the experimentally derived and theoretically calculated pK_a values provides solid support for the acid–base reactions proposed in this work.     

On the influence of dimerisation of lumiflavin in aqueous solution on its optical spectra – a quantum chemical study

The solvent effects on the photophysical and photochemical properties of lumiflavin are studied. By comparing different models for the aqueous environment including gas-phase ab-initio calculations, explicit solvation, continuum solvation model and QM/MM simulations the different aspects of solvation are singled out and analysed in detail. Dimerisation of flavins and its effects on the absorption and emission spectrum of flavins are studied using quantum chemical methods. The absorption and emission spectra of lumiflavin in water are compared to the properties of dimeric lumiflavin and to available experimental data.     

Mustard gas adsorption on the pristine and BN-doped graphynes: A computational study

The electronic sensitivity and reactivity of pristine, and BN doped graphyne (BNG) are scrutinized toward mustard gas using DFT calculations. The mustard gas weakly adsorbs via its Cl atom on the graphyne with adsorption energy about -3.1 kcal/mol and has no effect on its electrical conductivity. Replacing –C≡C– linkages with isoelectronic –BN– linkages increases the HOMO-LUMO gap (E_g) and decreases the work function and reactivity of graphyne. By mustard adsorption, the E_g of BNG decreases from 2.24 to 1.12 eV, increasing the electrical conductivity. Also, the BNG work function is considerably affected, changing the field emission electron current. Finally, a short recovery time about 0.03 s at room temperature is predicted for the mustard desorption from the surface of BNG. We also showed that the electrical conductivity change relates to the mustard concentration. The results indicate that the BNG may be a promising sensor for mustard gas.     

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.     

Dynamics of conformations,hydrogen bonds and translational diffusion of poly(methacrylic acid) in aqueous solution and the concentration transition in MD simulations

The dynamic behaviour of chain conformations, hydrogen bonds and translational diffusion of aqueous poly(methacrylic acid) (PMA) solution as a function of polymer volume fraction Φ_p across dilute to concentrated regimes inclusive of the pure polymer amorphous state was studied by molecular dynamics simulations. The behaviour of the relaxation time (τ) of the backbone dihedral angle auto-correlation function (ACF) reveals slower relaxation at higher level of polymer concentration and the existence of a concentration-driven relaxation transition for the aqueous polymer solution which occurs in the polymer volume fraction range, specifically 54% < Φ_p < 82% for this system. The relaxation constant τ for backbone dihedral angle exhibits a linear variation with Φ_p, indicating a first-order kinetic transition. The intermittent ACF for decay of the H-bond correlation shows that H-bonds among water molecules relax faster than those of the PMA–PMA and PMA–water type. The relaxation rate of PMA–water H-bonds shows a decrease up to Φ_p = 72% and becomes faster at Φ_p = 82% due to the confining influence of neighbouring PMA chains. PMA–water and water–water H-bond dynamics show transitions around Φ_p = 72% PMA. With increase in Φ_p PMA diffusion coefficient decreases exponentially and water diffusion coefficient decreases linearly, in agreement with experimental observations using fluorescence and nuclear magnetic resonance (NMR) spectroscopic studies.     

Influence of external magnetic field on the etching of a steel ball in an aqueous solution of nitric acid

The effect of change of shape of a steel ball was revealed as a result of its etching in an aqueous solution of nitric acid under influence of an external magnetic field. The elongation of a ferromagnetic ball was observed along the direction of an external magnetic field while etching took place uniformly in all the directions without magnetic field application. The steel ball etching in a magnetic field is characterized by formation of three cylindrically symmetric regions with different etching rates and surface structures, divided from each other by clear borders (namely, the pole, equator and transition regions are formed). The non-monotone dependences of etching rate, surface structure of a sample and sample shape after etching on an external magnetic field are observed.     

Proton shuffling in acid/base‐catalyzed enolizations: a computational study

Enolization of acetaldehyde catalyzed by the combined action of a general base (ammonia) and a general acid (formic acid) was examined by density functional theory at the B3LYP/6‐311 + G(3df,2p) level while manipulating distance relationships among the reactants. Computations were carried out in the gas phase, in the presence of four water molecules, and with a dielectric constant of 78.4. Enolization involves an early transition state where general‐base catalysis is more developed than general‐acid catalysis. Although formic acid does not promote enolization by itself, it does facilitate α‐proton transfer from acetaldehyde to the general base by several orders of magnitude. Formic acid accomplishes this feat via a hydrogen bond at a van der Waals distance to the carbonyl oxygen as opposed to forming a low‐barrier hydrogen bond. A low‐barrier hydrogen bond would indeed be capable of accelerating the enolization were it not for the energy cost of generating it. Formic acid may also facilitate enolization by internal solvation of the ammonium ion that is partially formed in the transition state via carbon‐to‐nitrogen proton transfer. General‐base catalysis by trimethylamine, which is out of position to coordinate with the formic acid carboxyl, actually has lower activation energy than that of ammonia catalysis, possibly owing to basicity/shielding effects. Computations also demonstrate that the proton removed by the ammonia nitrogen remains on the nitrogen throughout rather than being transferred via low‐energy rotation processes and secondary proton transfers to an oxygen atom of formic acid or the enol itself. Finally, stepwise and concerted mechanisms for enolizations have been proposed in the literature, with experimental evidence being provided for both. The concerted/non‐concerted disagreement seems to stem from the continuum of organic mechanisms that Nature bestows onto organic chemistry. Thus, acid/base catalysis varies from stepwise at one extreme to synchronous at the other extreme with an infinite number of concerted mechanisms in between. Since the degree of concertedness undoubtedly depends upon the particular acid, base, substrate, and solvent, disparate enolization models are to be expected. Copyright © 2012 John Wiley & Sons, Ltd.     

The anionic chain process mechanism for reactions of perchlorofluoroethanes with nucleophiles in solution: a theoretical study

Anionic chain process mechanism (including reactions (1)–(4)) suggested by the experimental investigations for the reactions of nucleophile (CH₃O^?) with perchlorofluoroethanes CF₂ClCCl₃ ( 1 ), CF₂ClCCl₂F ( 2 ), and CF₃CCl₃ ( 3 ) in solution is examined by performing calculations using the B3LYP method and the SCIPCM (self‐consistent isodensity polarizable continuum) model for simulating solution effects. The SCIPCM‐B3LYP calculations indicate that anionic species have large solvation energies and solvation energy values for different kinds of anions are quite different, which effects changes in ΔH's for the reactions in solution. Competition between anionic hyperconjugation and solvation leads to negative ΔH values for reactions (2) from 1 and 2 in solution. Reactions (3) and (4) from 1 , 2 , and 3 in solution are predicted to be exothermic or highly exothermic. Since the ΔH values for reactions (1) and (2) from 1 and 2 in solution are negative or small positive values, the reactions of CH₃O^? with 1 and 2 in solution proceed via the anionic chain process. For 3 in solution, reactions (1) and (2) are endothermic while reactions (3) and (4) are exothermic or highly exothermic. The reactions of CH₃O^? with 3 in solution may proceed via the anionic chain process. All these conclusions are in agreement with the experimental indications for reactions of nucleophiles with 1 , 2 , and 3 in solution. Copyright © 2007 John Wiley & Sons, Ltd.