Theoretical study of the kojic acid structure in gas phase and aqueous solution

Density functional calculations at the B3LYP/6‐311++G** level have been performed to determine the ground‐state conformational preference for kojic acid, a widely used skin‐whitening, antibrowning, and antibacterial agent. It is found that the gas phase consists almost entirely of the 5‐hydroxy‐2‐(hydroxymethyl)‐4H‐pyran‐4‐one tautomer, although several rotamers of this are prevalent. In aqueous solution, however, other tautomers are also present. The validity of the calculations is confirmed by the observed FTIR, NMR, and UV–vis spectra, which show good correspondence with the theoretical spectra. The electronic interactions are interpreted in terms of charge and bond order analysis as well as the composition of the HOMO and LUMO. The calculations show that kojic acid has partial aromatic character and is a good nucleophile. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Theoretical study in gas phase of linear and nonlinear optical properties of the ortho-, meta- and para-nitrophenol isomers

The linear (α), and nonlinear (β, γ) optical NLO properties of ortho-, meta- and para-nitrophenol (ONP, MNP and PNP) isomers have been calculated in gas phase by using ab initio (HF, MP2 and MP4) and density functional theory (DFT) (B3LYP, CAM-B3LYP) methods, with the 6-31+G(d,p) and 6-311+G(3d,3p) standard and the Sadlej specialized basis sets. These properties were evaluated both at static and at dynamic regime within the finite field FF numerical techniques and the time-dependent-Hartree–Fock approach at 1,910 nm, respectively. Additional calculations were performed for the β static hyperpolarizability of these isomers in presence of p-dioxane solvent with the Onsager Model and the SCRF-PCM approach, using B3LYP/6-31+G(d,p) and MP2/6-31+G(d,p) levels of theory. Additionally, CCSD/6-31+G(d,p) calculations were performed for the α, β and γ properties of PNP isomer. The B3LYP and MP2 α _ave results of the nitrophenol isomers are comparable to the experimental α _ave reports; while the tendency for the β _v calculated values (β _v PNP > β _v MNP > β _v ONP), that can be explained in terms of the O _x atomic charge of the –NO₂ group, does not follow exactly the experimental ones. The B3LYP γ _ave results are in correspondence to the experimental measurements, the correlation of which is r ² = 0.99. The use of FF methodology in conjunction with the B3LYP and MP2 methods and the 6-31+G(d,p) basis set show to be appropriate approaches to predict qualitative optical properties of Push–Pull like organic molecules, provided are considered the solvent effects or frequency dependence. However, to have a clear picture of the NLO properties of an isolated molecule, higher order correlation effects combined with specialized basis sets, frequency and solvent effects should be employed. We have demonstrated that MP4/Sadlej level of theory is able to reproduce NLO properties that can be considered equivalent to those from more sophisticated approaches, such as CCSD together with extended basis sets.     

Quantum-chemical study of the mechanism of the hydrolysis of amides in the gas phase and in aqueous solution

The MNDO, AM1, and MNDO/M methods have been used to calculate the profile of the potential energy surface for the hydrolysis of formamide in the gas phase and in aqueous solution. Estimates have been made of the changes in the energy barrier in specific acid and base catalysis, and it is shown that in the absence of proton exchange between the reacting system and the solvent the interaction of the charged reactants with a polar medium impedes the reaction.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 8, pp. 1785–1792, August 1989.     

Theoretical study of reaction mechanisms for the ketonization of vinyl alcohol in gas phase and aqueous solution

Theoretical ab initio calculations are done on different mechanisms for the conversion of vinyl alcohol to acetaldehyde, both in gas phase and in solution. Several basis sets are used in order to assess the accuracy of the results in gas phase and a continuum model of the solvent is employed to mimic reactions in water solution. The results indicate a catalytic action of water in hydrated clusters in gas phase, whereas in solution, and within the error limits of our calculations, both neutral water-chain and ionic mechanisms appear to be equally probable. Finally, the action of acids or bases is tested through the analysis of the reaction of vinyl alcohol with H₃O⁺ and HO^–. The results of the calculations are shown to be in qualitative agreement with the experimental facts when 6-31++G basis set is used but not when either STO-3G or 4-31G basis sets are employed.     

Theoretical studies on the hydrolysis of mono-phosphate and tri-phosphate in gas phase and aqueous solution

Phosphate hydrolysis by GTPases plays an important role as a molecular switch in signal transduction and as an initiator of many other biological processes. Despite the centrality of this ubiquitous reaction, the mechanism is still poorly understood. As a first step to understand the mechanisms of this process, the nonenzymatic hydrolysis of mono-phosphate and tri-phosphate esters were systematically studied in gas phase and aqueous solution using hybrid density functional methods. The dielectric effect of the environment on the energetics of these processes was also explored. Theoretical results show that for mono-phosphate ester, the dissociative pathway is much more favorable than the associative pathway. However, the reaction barriers for the dissociative and associative pathways of tri-phosphate hydrolysis are very close in aqueous solution, though the dissociative pathway is more favorable in the gas phase. High dielectric solvents, such as water, significantly lower the activation barrier of the associative pathway due to the greater solvation energy of the associative transition states than that of the reactant complex. By contrast, the barrier of the dissociative pathway, with respect to the gas phase, is less sensitive to the surrounding dielectric. In the associative hydrolysis pathway of the tri-phosphate ester, negative charge is transferred from the gamma-phosphate to beta-phosphate through the bridging ester oxygen and results in Pgamma-O bond dissociation. No analogous charge transfer was observed in the dissociative pathway, where Pgamma-O bond dissociation resulted from proton transfer from the gamma-phosphate to the bridge oxygen. Finally, the active participation of local water molecules can significantly lower the activation energy of the dissociative pathway for both mono-phosphate and tri-phosphate.     

Theoretical study on the gas phase reaction of dimethyl sulfoxide with atomic chlorine in the presence of water

We have investigated theoretically the gas phase reactions of dimethyl sulfoxide (DMSO) with atom Cl in the absence and presence of a single water molecule. The calculations of the potential energy surfaces in the water-free and water-assisted along the different channels are performed at the CCSD(T)/6-311++G(2df,2p)//MP2/6-31G(d) level. The calculated results show that energy barriers of the H_c-abstraction reaction are reduced due to one water molecule added. The computed rate constants of H_c-abstraction reaction indicate that the reaction with water is faster than the value of the naked reaction. However, H_a-abstraction reaction, path2, path3, and path4 are slower without water than hydrous channels.     

Theoretical study of morphine and heroin: Conformational study in gas phase and aqueous solution and electron distribution analysis

The conformational preferences of morphine and heroin were studied in gas phase and with inclusion of solvent effects. At 298.15 K, three conformers are significant for isolated morphine, all of them displaying antiperiplanar arrangement for the C2? C3? O? H unit, and there is only one significantly populated conformer for heroin. Quantum theory of atoms in molecules analysis of the electron density in their most populated conformers in gas phase indicates that the positive charge is shared among the amino hydrogen, those hydrogens of the methylamino group, and all of the hydrogens attached to the bridgehead carbons. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2472–2482, 2010     

Theoretical investigation of the proton affinities of benzazoles in the gas phase and in solution

The ground‐state equilibrium geometries of benzothiazole, benzoxazole, and benzimidazole were optimized at the density functional theory (DFT)/6‐31G** level of theory. Proton affinities on each of the possible sites in the studied series of compounds have been calculated at the DFT/6‐31G**/6‐311++G** level. The results indicate clearly that N‐site protonation is strongly favored over X‐site protonation (X = NH, O, S) for the series studied. Correlation of the computed proton affinities to the energy (E_HOMO) of the highest occupied MO in the gas phase and in solution has been explored and discussed. A comprehensive investigation of the effect of solvent on the process of protonation of the studied compounds has been performed. Different dielectric continuum models (i.e., Onsager, PCM, and IPCM) have been tested; their performance and range of applicability are reported and discussed. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Theoretical study on the reaction of methane and zinc oxide in gas phase

The mechanism of the reaction between CH₄ and ZnO has been studied theoretically at the CCSD(T)//B3LYP/6-311++G(2d,2p) levels. Four possible reaction pathways, yielding three products of syngas, HCHO and CH₃OH, respectively, have been evaluated. All the four pathways are predicted to occur via the formation of CH₄ZnO molecular complex with two H atoms of CH₄ approaching to the Zn end of ZnO. From this complex, the insertion of ZnO into the CH bond of CH₄ might proceed through two concerted manners along with charge transfer process. The pathway corresponding to the production of syngas is energetically feasible, in which the cleavage of CH and ZnH bonds with the formation of H₂ molecule is predicted to be the rate-limiting-step with the energy barrier of 45.4 kcal/mol.     

Theoretical study of the relative stability of rotational conformers of alpha and beta-D-glucopyranose in gas phase and aqueous solution

The alpha-beta anomer energy difference and the stability of 10 rotamers of counterclockwise D-glucopyranose were studied in vacuo and in aqueous solution at the B3LYP/6-31+G(d,p) level. To obtain the solute charge distribution and the solvent structure around it, we used the averaged solvent electrostatic potential from molecular dynamics method, ASEP/MD, which alternates molecular dynamics and quantum mechanics calculations in an iterative procedure. The main characteristics of the anomeric equilibrium, both in vacuo and in solution, are well reproduced. The relative stability of the different anomers is related to the availability of the free pairs of electrons in the anomeric oxygen to interact with the water molecules. The influence of solvation in the conformer equilibrium is also analyzed.     

Theoretical studies on the reaction of pentafulvenone with water in gas phase and aqueous solvent

In gas phase, the hydrations of pentafulvenone to generate three types of cyclopentadienyl carboxylic acids are studied theoretically at the MP2/6-311+G**//B3LYP/6-311+G** level. A water molecule attacking the C=O double bond of pentafulvenone can yield cyclopentadienyl carboxylic acids via the formation of fulvenediols, and attacking the C=C double bond of pentafulvenone can directly yield cyclopentadienyl carboxylic acid. The barriers of rate-determining transition states are 42.2 and 30.4 kcal mol⁻¹, respectively. The barriers of rate-determining transition states for two water molecules system are 20.2 and 19.6 kcal mol⁻¹, respectively. The products can isomerize to each other. In aqueous solvent, the hydrations of pentafulvenone are investigated using PCM-UAHF model at the MP2 (PCM)/6-311+G**// B3LYP (PCM)/6-311+G** and MP2 (PCM)/6-311+G**// B3LYP/6-311+G** levels. The barriers of all rate-determining transition states are decreased. The added water molecule acts as catalyst in both gas phase and aqueous solvent. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Theoretical studies of the tautomeric equilibria for five-member N-heterocycles in the gas phase and in solution

Tautomeric equilibria have been studied for five-member N-heterocycles and their methyl derivatives in the gas phase and in different solvents with dielectric constants of epsilon = 4.7-78.4. The free energy changes differently for tautomers upon solvation as compared to the gas phase, resulting in a shift of the equilibrium constant in solution. Solvents with increasing dielectric constant produce more negative solute-solvent interaction energies and increasing internal energies. The methyl-substituted imidazole and pyrrazole form delicate equilibria between two tautomeric forms. Depending on the solvent, the methyl-substituted triazoles and tetrazole have one or two major tautomers in solution. When estimating the relative solvation free energies by means of an explicit solvent model and using the FEP/MC method, one observes that the preferred tautomers differ in several cases from those predicted by the continuum solvent model. The 1,2-prototropic shift, as an intramolecular tautomerization path, requires about 50 kcal/mol activation energy for imidazole in the gas phase, and this route is also disfavored in a solution. The calculated activation free energy along the intramolecular path is 48-50 kcal/mol in chloroform and water as compared to a literature value of 13.6 kcal/mol for pyrrazole in DMSO. A molecular dynamics computer experiment favors the formation of an imidazole chain in chloroform, making the 1,3-tautomerization feasible along an intermolecular path in nonprotic solvents. In aqueous solution, one strong N-H...Ow hydrogen bond is formed for each species, whereas all other nitrogens in the ring form weaker, N...HwOw type hydrogen bonds. The tetrahydrofuran solvent acts as a hydrogen bond acceptor and forms N-H...Oether bonds. Molecules of the dichloromethane solvent are in favorable dipole-dipole interactions with the solute. The results obtained are useful in the design of N-heterocyclic ligands forming specified hydrogen bonds with protein side chains.     

Excited state proton transfer in guanine in the gas phase and in water solution: a theoretical study

Theoretical investigations were performed to study the phenomena of ground and electronic excited state proton transfer in the isolated and monohydrated forms of guanine. Ground and transition state geometries were optimized at both the B3LYP/6-311++G(d,p) and HF/6-311G(d,p) levels. The geometries of tautomers including those of transition states corresponding to the proton transfer from the keto to the enol form of guanine were also optimized in the lowest singlet pipi* excited state using the configuration interaction singles (CIS) method and the 6-311G(d,p) basis set. The time-dependent density function theory method augmented with the B3LYP functional (TD-B3LYP) and the 6-311++G(d,p) basis set was used to compute vertical transition energies using the B3LYP/6-311++G(d,p) geometries. The TD-B3LYP/6-311++G(d,p) calculations were also performed using the CIS/6-311G(d,p) geometries to predict the adiabatic transition energies of different tautomers and the excited state proton transfer barrier heights of guanine tautomerization. The effect of the bulk aqueous environment was considered using the polarizable continuum model (PCM). The harmonic vibrational frequency calculations were performed to ascertain the nature of potential energy surfaces. The excited state geometries including that of transition states were found to be largely nonplanar. The nonplanar fragment was mostly localized in the six-membered ring. Geometries of the hydrated transition states in the ground and lowest singlet pipi* excited states were found to be zwitterionic in which the water molecule is in the form of hydronium cation (H3O(+)) and guanine is in the anionic form, except for the N9H form in the excited state where water molecule is in the hydroxyl anionic form (OH(-)) and the guanine is in the cationic form. It was found that proton transfer is characterized by a high barrier height both in the gas phase and in the bulk water solution. The explicit inclusion of a water molecule in the proton transfer reaction path reduces the barrier height drastically. The excited state barrier height was generally found to be increased as compared to that in the ground state. On the basis of the current theoretical calculation it appears that the singlet electronic excitation of guanine may not facilitate the excited state proton transfer corresponding to the tautomerization of the keto to the enol form.     

Theoretical mechanism study of UF6 hydrolysis in the gas phase

The mechanism of the gas-phase reaction UF 6 + H 2O --> UOF 4 + 2HF is explored using relativistic density functional theory calculations. Initially, H 2O coordinates with UF 6 to form a 1:1 complex UF 6.H 2O. Over an activation energy barrier of about 19 kcal/mol, H 2O transfers a H atom to a nearby ligand F, resulting in UF 5OH + HF. The eliminated HF or another H 2O molecule may form a hydrogen bond with UF 5OH. Starting from UF 5OH, the second HF elimination results in UOF 4. If UF 5OH is in the isolated form, UF 5OH --> UOF 4 + HF takes place over a barrier of 24 kcal/mol. If UF 5OH is hydrogen-bonded with H 2O or HF, the conversion barrier is less than 10 kcal/mol. Once formed, the unstable UOF 4 tends to associate with additional ligands and hydrogen-bonding donors. The calculated binding energies indicate the significance of such interactions, which may have profound impact on further HF eliminating reactions. The IR spectra features can be used to indicate the formation and interaction type of the intermediates and products.     

Theoretical studies of the structure and stability of protonated olefins in the gas phase and in solution

The calculation of carbenium and carbonium type cations resulting from the protonation of olefins with growing length and increasing chain branching was carried out by quantum chemical methods which were tested elsewhere.One result is the distinction of olefins with an equal number of alkyl substituents on both sides of the double bond and other ones with different number. In the latter case generally no bridged structures could be defined.The influence of nucleophilic solvents on the stability of the cationic structures is simulated on the basis of Klopman's solvaton model. These calculations show that solvents may change the gas phase data in a remarkable way.     

Theoretical conformational analysis for neurotransmitters in the gas phase and in aqueous solution. Norepinephrine

The natural neurotransmitter (R)-norepinephrine takes the monocationic form in 93% abundance at the physiological tissue pH of 7.4. Ab initio and DFT/B3LYP calculations were performed for 12 protonated conformers of (R)-norepinephrine in the gas phase with geometry optimizations up to the MP2/6-311++G level, and with single-point calculations up to the QCISD(T) level at the HF/6-31G-optimized geometries. Four monohydrates were studied at the MP2/6-31G//HF/6-31G level. In the gas phase, the G1 conformer is the most stable with phenyl.NH(3)(+) gauche and HO(alc).NH(3)(+) gauche arrangements. A strained intramolecular hydrogen bond was found for conformers (G1 and T) with close NH(3)(+) and OH groups. Upon rotation of the NH(3)(+) group as a whole unit about the C(beta)-C(alpha) axis, a 3-fold potential was calculated with free energies for barriers of 3-12 kcal/mol at the HF/6-31G level. Only small deviations were found in MP2/6-311++G single-point calculations. A 2-fold potential was calculated for the phenyl rotation with free energies of 11-13 kcal/mol for the barriers at T = 310 K and p = 1 atm. A molecular mechanics docking study of (R)-norepinephrine in a model binding pocket of the beta-adrenergic receptor shows that the ligand takes a conformation close to the T(3) arrangement. The effect of aqueous solvation was considered by the free energy perturbation method implemented in Monte Carlo simulations. There are 4-5 strongly bound water molecules in hydrogen bonds to the conformers. Although hydration stabilizes mostly the G2 form with gauche phenyl.NH(3)(+) arrangement and a water-exposed NH(3)(+) group, the conformer population becomes T > G1 > G2, in agreement with the PMR spectroscopy measurements by Solmajer et al. (Z. Naturforsch. 1983, 38c, 758). Solvent effects reduce the free energies for barriers to 3-6 and 9-12 kcal/mol for rotations about the C(beta)-C(alpha) and the C(1)(ring)-C(beta) axes, respectively.     

Theoretical study on the gas phase reaction of acrylonitrile with atomic hydrogen

The complex potential energy surface of the H + CH₂=CHCN reaction has been investigated at the BMC-CCSD level based on the geometric parameters optimized at the BHandHLYP/6-311++G(d,p) level. This reaction is revealed to be one of the significant loss processes of acrylonitrile. The BHandHLYP and M05-2X methods are employed to obtain initial geometries. The reaction mechanism confirms that H can attack on the C=C double bond or C and N atom of –CN group to form the chemically activated adducts IM1 (CH₃CHCN), IM2 (CH₂CH₂CN), IM3′ (CH₂=CHCHN) and IM5 (CH₂=CHCNH), and direct H-abstraction paths may also occur. Temperature- and pressure-dependent rate constants have been carried out using Rice–Ramsperger–Kassel–Marcus theory with tunneling correction. IM1 (CH₃CHCN) formed by collisional stabilization is the major product at the 760 Torr pressure of H₂ and in the temperature range (200–1,600 K); whereas the production of IM2 (CH₂CH₂CN) is the main channel at 1,600–3,000 K. The calculated rate constants are in good agreement with the experimental data.     

Theoretical studies on the hydrolysis of phosphate diesters in the gas phase,solution, and RNase A

Density functional theory, polarizable continuum models and semiempirical hybrid quantum mechanical/molecular mechanical (QM/MM) calculations were applied to the hydrolysis of phosphate diesters in the gas phase, in solution, and in the enzyme RNase A. Neutralization of the negative charge of the pentacovalent phosphorane intermediates provides a substantial stabilization of the transition‐state structures in the gas phase. Inclusion of solvent effects on the phosphate/phosphorane species was critical to reproducing the trends in reactivity observed experimentally. Finally, the catalytic mechanism for the hydrolysis of uridine 2′,3′‐cyclic phosphate by RNase A was studied by QM/MM calculations. Our results suggest that the rate‐limiting transition state of the reaction corresponds to the approach of a water molecule to the phosphate and its activation by His119. Thus, His119 acts as a generalized base for the reaction. The water attack leads to a pentacovalent phosphorane transition state of formal charge ?2; this excess of negative charge in the transition state is stabilized by a number of positively charged residues including His12 and Lys41. In the second stage of the reaction, the phosphorane is converted into products. This part of the reaction proceeds without a detectable barrier, and it is facilitated by a proton transfer from Lys41 to the departing O_2′. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution

We are presenting a theoretical study of the hydrolysis of a β‐lactam antibiotic in gas phase and in aqueous solution by means of hybrid quantum mechanics/molecular mechanics potentials. After exploring the potential energy surfaces at semiempirical and density functional theory (DFT) level, potentials of mean force have been computed for the reaction in solution with hybrid PM3/TIP3P calculations and corrections with the B3LYP and M06‐2X functionals. Inclusion of the full molecule of the antibiotic, Cefotaxime, in the gas phase molecular model has been demonstrated to be crucial since its carboxylate group can activate a nucleophilic water molecule. Moreover, the flexibility of the substrate implies the existence of a huge number of possible conformers, some of them implying formation of intramolecular hydrogen bond interaction that can determine the energetics of the conformers defining the different states along the reaction profile. The results show PM3 provides results that are in qualitative agreement with DFT calculations. The free energy profiles show a step‐wise mechanism that is kinetically determined by the nucleophilic attack of a water molecule activated by the proton transfer to the carboxylate group of the substrate (the first step). However, since the main role of the β‐lactamase would be reducing the free energy barrier of the first step, and keeping in mind the barrier obtained from second intermediate to products, population of this second intermediate could be significant and consequently experimentally detected in β‐lactamases, as shown in the literature. © 2012 Wiley Periodicals, Inc.     

Optical properties of protonated Rhodamine 19 isomers in solution and in the gas phase

Visible light absorption and fluorescence of three positional isomers of protonated Rhodamine 19 (o-, m- and p-R19H(+)) were studied in solution and in the gas phase. In solution, strong solvatochromic effects lead to spectral shifts between rhodamine isomers. In contrast, in the gas phase, these species were found to exhibit very similar fluorescence, while pronounced differences were observed in the absorption spectra. The o-R19H(+) was found to have the largest Stokes shift in the gas phase (around 10 nm), suggesting that an intramolecular relaxation operates in the excited electronic state for this isomer. Several mechanisms for this relaxation are proposed, such as the change of the dihedral angle between the carboxyphenyl group and the xanthene chromophore or that between the carboxylic group and the phenyl ring.