Calculation of dissociation constants and chemical hardness of some biologically important molecules: A theoretical study

The gas‐phase geometries of neutral, protonated, and deprotonated forms of some biologically important molecules, alanine (Ala), glycine (Gly), phenylalanine (Phe), and tyrosine (Tyr), were optimized using density functional theory at B3LYP/6‐311++G(d) and the ab initio HF/6‐311++G(d) level of theories. The neutral and different stable ionic states of Ala, Gly, Phe, and Tyr have also been solvated in aqueous medium using polarizable continuum model for the determination of solvation free energies in the aqueous solution. The gas‐phase acidity constants of above four molecules have been also calculated at both levels of theories and found that the values calculated at HF/6‐311++G(d) method are in good agreement with experimental results. A thermodynamic cycle was used to determine the solvation free energies for the proton dissociation process in aqueous solution and the corresponding pK_a values of these molecules. The pK_a values calculated at B3LYP/6‐311++G(d) method are well supported by the experimental data with a mean absolute deviation 0.12 pK_a units. Additionally, the chemical hardness and the ionization potential (IP) for these molecules have been also explored at both the level of theories. The Tyr has less value of chemical hardness and IP at both levels of theories compared with other three molecules, Ala, Gly, and Phe. The calculated values of chemical hardness and IP are decreasing gradually with the substitution of the various functional groups in the side chain of the amino acids. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

The Role of Intramolecular Hydrogen Bonds vs. Other Weak Interactions on the Conformation of Hyponitrous Acid and Its Mono- and Dithio-Derivatives

High level ab initio and density functional theory calculations have been carried out to investigate the relative stability of the different conformers of hyponitrous acid and its mono- and dithio-derivatives. Geometries and vibrational frequencies were obtained at the B3LYP/6-311+G(d,p) level and final energies through B3LYP/6-311++G(3df,2pd) single point calculations. The reliability of this theoretical scheme has been assessed by comparing these DFT results with those obtained at the G3 level of theory, for some suitable cases. The cis conformers of hyponitrous acid and its mono- and dithio-derivatives are systematically more stable than the trans ones because in the cis conformation a dative interaction between the nitrogen-lone pairs and the σ_NX^* antibonding orbital is significantly favored. Quite interestingly, in general, the conformers presenting an intramolecular hydrogen bond (IHB) are not the global minima of the corresponding potential energy surfaces and only for hyponitrous acid the conformer with a OH ⋅s O IHB is slightly more stable than the cis conformer without IHB. The low stability of the tautomers with IHB is closely related with another weak intramolecular interaction which involves the lone-pairs of the chalcogen atoms and the π_NN^* antibondig orbital, and which is significantly perturbed when the IHB is formed.     

Theoretical studies of uracil–(H2O)n (n = 1–7) clusters by ab initio and ABEEMσπ/MM fluctuating charge model

Uracil–(H₂O)_n (n = 1–7) clusters were systemically investigated by ab initio methods and the newly constructed ABEEMσπ/MM fluctuating charge model. Water molecules have been gradually placed in an average plane containing uracil. The geometries of 38 uracil–water complexes were obtained using B3LYP/6-311++G** level optimizations, and the energies were determined at the MP2/6-311++G** level with BSSE corrections. The ABEEMσπ/MM potential model gives reasonable properties of these clusters when comparing with the present ab initio data. For interaction energies, the root mean square deviation is 0.96 kcal/mol, and the linear coefficient reaches 0.997. Furthermore, the ABEEMσπ charges changed when H₂O interacted with the uracil molecule, especially at the sites where the hydrogen bond form. These results show that the ABEEMσπ/MM model is fine giving the overall characteristic hydration properties of uracil–water systems in good agreement with the high-level ab initio calculations.     

Density functional theoretical study of pKa of RCOOH (RH,CH3, and C2H5) using the combination of the extended clusters‐continuum model

The accurate pK_a determinations for three carboxylic acids have been investigated using the combination of the extended clusters‐continuum model at B3LYP/6‐31+g(d,p) and B3LYP/6‐311++g(d,p) levels. To take into account of the effect of the water combined with carboxylic acids in different positions, eleven molecular clusters were considered. Among these clusters, the one involving the carboxylic acid wrapped up with water molecules and saturated with hydrogen bonds (four hydrogen bonds around ? COOH) leads to the best B3LYP pK_a results compared to the experimental data. For those clusters saturated with hydrogen bonds, when n = 3 (the number of water molecules), the average absolute errors between the calculated pK_a results and experimental data of these three carboxylic acids were 0.19 (0.23) and 0.12 (0.22) pK_a at B3LYP/6‐31+g(d,p)//PCM (IEFPCM) and B3LYP/6‐311++g(d,p)//PCM (IEFPCM) levels, respectively; when n = 4, they are 0.53 (1.23) and 1.09 (1.03) pK_a, respectively. On the basis of the above results, the molecular cluster saturated with four hydrogen bonds formed by three waters and one carboxylic acid molecule was the chief existence in the carboxylic acid solution. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Structures and stabilities of HPO<Subscript>2</Subscript> isomers

The potential energy surface of HPO₂ system including eight isomers and twelve transition states is predicated at MP2/6-311++G(d, p) and QCISD(t)/6-311++G(3df,2p)(single-point) levels of theory. On the potential energy surface, cis-HOPO(E1) is found to be thermodynamically and kinetically most stable isomer followed by trans-HOPO(E2) and HPO(O)(C_2v, E3) at 10.99 and 48.36 kJ/mol higher, respectively. Based on the potential energy surface, only E1 and E3 are thermodynamically stable isomers, and should be experimentally observable. The products cis-HPOO(E5) and trans-HPOO(E6) in the first-step reaction of HP with O₂ can isomerize into isomer E1 that has higher stability. The reaction of OH with PO will directly lead to the formation of isomer E1. The computed results are well consistent with the previous experimental studies.     

Theoretical study of the reaction of CF3O radicals with CO

The potential energy surface for the reaction of the CF₃O radicals with CO was investigated. The geometries and vibrational frequencies of the reactants, transition states, intermediates, and products were calculated at the UB3LYP/6-311+G(2d,p), UB3LYP/6-311+G(3df,2p) and UMP2/6-311+G(2d,p) levels of theory. The energies were improved by using the G2M(CC2) and G3B3 methods. The calculation suggests the reaction proceeds via either the fluorine abstraction of CF₃O by CO to produce FCO + CF₂O with a high energy barrier or the barrierless association of the reactants to form the trans-CF₃OCO intermediate. The trans-CF₃OCO is predicted to undergo subsequent isomerization to cis-CF₃OCO or dissociate directly to the products FCO + CF₂O and CF₃ + CO₂. The collisional stabilization of trans-CF₃OCO is dominant at room temperature, while trans-CF₃OCO isomerizing to cis-CF₃OCO followed by dissociating to CF₃ + CO₂ is accessible when temperature rises. The reason for only trans-CF₃OCO without cis-CF₃OCO observable in Ashen’s experiment [S.V. Ahsen, J. Hufen, H. Willner, J.S. Francisco, Chem. Eur. J. 8 (2002) 1189] is cis-CF₃OCO can be produced only via the isomerization of trans-CF₃OCO, and its yield is inappreciable at a low experimental temperature. The enthalpies of formation for the two conformations of CF₃OCO have been deduced: (trans-CF₃OCO) = −196.25 kcal mol⁻¹, (trans-CF₃OCO) = −197.46 kcal mol⁻¹, (cis-CF₃OCO) = −193.64 kcal mol⁻¹, and (cis-CF₃OCO) = −194.90 kcal mol⁻¹.     

Computational study of keto–enol equilibria of tropolone in gas and aqueous solution phase

Density functional theory calculations employing the B3LYP exchange-correlation functional, as well as Hartree–Fock computations, were performed on 2-hydroxy-2,4,6-cycloheptatrien-1-one (tropolone) and 3,5- and 3,6-cycloheptadiene-1,2-dione in gas and aqueous solution phases in order to determine the equilibrium constant for keto to enol interconversion of the isomers of C₇H₆O₂. Two standard basis sets were used throughout, namely 6-311++G^∗∗ and aug-cc-pVDZ. Solvent effects were modelled using two different self-consistent reaction field approaches – the Onsager dipole and the polarizable continuum models (PCM). In addition, the G3 method was used for calculations on species in the gas phase. Molecular geometries were fully optimized at each model chemistry, and it was found that the two keto isomers are always higher in energy than the enol form. From the results of B3LYP/6-311++G^∗∗ calculations of the difference in Gibbs free energy in the gas phase and using PCM, the relative pK values for the 2-hydroxy-2,4,6-cycloheptatrien-1-one ? 3,5- and 3,6-cycloheptadiene-1,2-dione system are 13.75 (g), 15.78 (g) and 13.05 (aq) and 13.45 (aq), respectively. That equilibrium is tilted almost exclusively in the direction of tropolone is due to resonance stabilization of the enol as a result of aromaticity, and is most easily understood on the basis of elementary Hückel theory.     

A quest for triplet silylenes XHSi3 at ab initio and DFT levels (X = H, F, Cl and Br)

Four ground state triplet silylenes are found among 30 possible silylenic XHSi₃ structures (X = H, F, Cl and Br), at seven ab initio and DFT levels including: B3LYP/6-311++G^∗∗, HF/6-311++G^∗∗, MP3/6-311G^∗, MP2/6-311+G^∗∗, MP4(SDTQ)/6-311++G^∗∗, QCISD(T)/6-311++G^∗∗ and CCSD(T)/6-311++G^∗∗. The latter six methods indicate that the triplet states of 3-flouro-1,2,3-trisilapropadienylidene, 1-chloro-1,2,3-trisilapropargylene and 3-chloro-1,2,3-trisilapropargylene are energy minima. These triplets appear more stable than their corresponding singlet states which cannot even exist for showing negative force constants. Also, triplet state of 1-flouro-1,2,3-trisilapropargylene is possibly accessible for being an energy minimum, since its corresponding singlet state is not a real isomer. Some discrepancies are observed between energetic and/or structural results of DFT vs. ab initio data.     

Structural properties and potential reactivity of substituted 3- aroyldithiocarbazates

A series of substituted 3-aroyldithiocarbazates has been synthesized and studied. The corresponding acid dissociation constants have been determined potentiometrically. Semiempirical PM3 molecular orbital calculations suggest the existence of several tautomeric forms of the compounds. Geometrical parameters, proton affinities, and static reactivity indices have been examined. Structural properties and protonation sites are well described by calculations. The strong correlations between the pK _a values and the Hammett constants as well as the N(3) calculated proton affinities indicate that the N(3) atom is the most probable protonation site. The thermodynamics of the protonation process are mainly controlled by HOMO-LUMO rather than electrostatic interactions. According to PM3 results, 3-aroyldithiocarbazic acid should be quite stable in the gas phase, while a mechanism for its decomposition in solution is proposed.     

Ab initio study on the mechanism of reaction HNCO+NH2

Ab initio UMP2 and UQCISD(T) calculations, with 6-311G** basis sets, were performed for the titled reactions. The results show that the reactions have two product channels: NH₂+ HNCO?NH₃+NCO (1) and NH₂+HNCO?N₂H₃+CO (2), where reaction (1) is a hydrogen abstraction reaction via an H-bonded complex (HBC), lowering the energy by 32.48 kJ/mol relative to reactants. The calculated QCISD(T)//MP2(full) energy barrier is 29.04 kJ/mol, which is in excellent accordance with the experimental value of 29.09 kJ/mol. In the range of reaction temperature 2300–2700 K, transition theory rate constant for reaction (1) is 1.68×10¹¹–3.29×10¹¹ mL·mol^-1·s^-1, which is close to the experimental one of 5.0×10¹¹mL·mol^-1·s^-1or less. However, reaction (2) is a stepwise reaction proceeding via two orientation modes,cis andtrans, and the energy barriers for the rate-control step at our best calculations are 92.79 kJ/mol (forcis-mode) and 147.43 kJ/mol (fortrans-mode), respectively, which is much higher than reaction (1). So reaction (1) is the main channel for the titled reaction.     

HNO自由基与O2反应机理的理论研究

采用密度泛函理论(DFT)和从头算方法,在B3LYP/6-311++G(d,p)水平上对反应HNO+O_2做了理论计算研究。优化得到了反应物、中间体、过渡态和产物的几何构型以及相应的能量值、振动频率。通过分析反应路径的能量差异,以及异构化难易程度,发现HNO+O_2反应有2种产物通道:HOONO和HNO_3。其中过氧亚硝酸HOONO是主要产物,有3种稳定的构象。     

A theoretical study of the interaction between [HB≡CH]<Superscript>−</Superscript>, [H<Subscript>2</Subscript>B=CH<Subscript>2</Subscript>]<Superscript>−</Superscript>, and boratabenzene anions with alkali and alkaline earth metals: properties and structures

The nature of [HB≡CH]⁻, [H₂B=CH₂]⁻, and boratabenzene interactions with alkaline and alkaline earth metals are studied by ab initio calculations. The interaction energies are calculated at the B3LYP/6-311++G(d,p) level. The calculations suggest that the cation size and charge are two influential factors that affect the nature of the interaction. AIM and NBO analyses of the complexes indicate that the variation of densities and the extent of charge transfers upon complexation correlate well with the obtained interaction energies.     

Hydrogen bond interactions at the TiO2 surface: Their contribution to the pH dependent photo-catalytic degradation of p-nitrophenol

We have obtained pK_a values of p-nitrophenol–TiO₂ by measuring the adsorption equilibrium constants of p-nitrophenol (PNP) on the TiO₂ surface at different pH values. These values have been obtained from Langmuir isotherms and from a plot of 1/rate vs. 1/[PNP]_o obtained during TiO₂ catalyzed solar light photo-degradation of PNP. Two limit equilibrium constants are readily obtained depending on the solution pH: at pH 5 at which the TiO₂ surface is mainly positively charged and at pH 8 when it is negatively charged. With these and other adsorption equilibrium constants and the PNP pK_a value in solution, thermodynamic cycles are established in order to obtain the PNP pK_a when it is adsorbed on positively charged, neutral and negatively charged TiO₂ surfaces. From these pK_a values useful information on the PNP–TiO₂ interaction is readily obtained. For instance, the PNP nitro group interacts with the TiO₂ surface via a hydrogen bond, arising from the complex of water molecules with the Ti⁴⁺ ions on its surface. The weaker the hydrogen bond donor, the stronger the oxygen nitro group basicity. Therefore, pK_a changes on the phenolic hydroxyl group result from these interactions. Linear free energy correlations, maximum PNP adsorption capacity values (Q_L) and FTIR ATR, spectrum support this proposal. A k_obs vs. pH degradation profile of p-nitrophenol is also provided.     

Quantum study on the electrocyclic reactions of CH2CHCHCHX (XH,F, Cl)

The microscopic mechanisms of the electrocyclic reactions for cis‐1,3‐butadiene and its monofluoro‐, monochloroderivatives have been studied by density functional theory (DFT), using the B3LYP method and 6‐311++G** basis sets. We optimized the geometric configurations of reactants, transition states, and products; verified all the probable transition states through vibrational analysis; and calculated the relative single‐point energies at the QCISD(T)/6‐311++G**//B3LYP/6‐311++G**. The results show that the monofluoro‐, monochloroderivatives of cis‐1,3‐butadiene both have two conformers; the reactant favors the electrocyclic reaction when one outboard hydrogen atom of the CH₂ groups is substituted by the fluorine or chlorine atom. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Theoretical study of electronic spectra of linear carbon clusters HC2nS (n = 1–5)

In this work we report the structures and stabilities of linear carbon clusters HC_2nS (n = 1–5) in their ground states using the B3LYP density functional. The rotational constants at the optimized geometries give excellent agreement with the experimental and previous theoretical values. The vertical excitation energies of the 2²Π ← X²Π transitions at the CASPT2 level are 3.16, 2.66, 2.05, 1.78, and 1.55 eV, respectively, in good agreement with the corresponding observed values of 3.01, 2.48, 2.10, 1.84, and 1.65 eV. Also, the exponential-decay curves for these vertical excitation energies obtained from experiments and theoretical calculations are illuminated.     

Optical rotation and two chiral C atoms of aliphatic cyclic dipeptides

Accurate geometries structures and total energies have been determined for the conformers of cyclo(L-Pro-Gly), cyclo(L-Ala-L-Ala), and cyclo(L-Pro-Ala) in the gaseous phase, using HF and B3LYP correlation methods at 6−31++G(d), 6−311++G(d, p), 6−311++G(2d, 2p) and aug-cc-pvdz basis sets. High level computations MP2 with 6−311++G(2d, 2p) basis set indicate that the relative stabilities of the available conformers can be determined correctly at the B3LYP/6−311++g(2d, 2p) level of theory. We have also described the implementation of DFT and HF theory for calculations of the optical rotation at 589.3 nm. In L-Ala-L-Ala, and L-Pro-Ala molecules, they have two chiral C (C*), so we discuss the different effect of two chiral C to optical activity of cydo(L-Pro-Gly), cyclo(L-Ala-L-Ala), and cyclo(L-Pro-Ala).     

Theoretical calculation of the pKa values of some drugs in aqueous solution

In this work, calculations of pK_a values have been performed on benzoic acid and its para‐substituted derivatives and some drugs by using Gaussian 98 software package. Gas‐phase energies were calculated with HF/6‐31 G** and B3LYP/6‐31 G** levels of theory. Free energies of solvation have been computed using the polarizable continuum model (PCM), conductor‐like PCM (CPCM), and the integral equation formalism‐PCM at the same levels which have been used for geometry determination in the gas‐phase. The results that show the calculated pK_a values using the B3LYP are better than those using the corresponding HF. In comparison to the other models, the results obtained indicate that the PCM model is a suitable solvation model for calculating pK_a values. For the investigated compounds, a good agreement between the experimental and the calculated pK_a values was also observed. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Ab initio and density functional theory study of the enthalpies of formation of F2SOx and FClSOx (x=1, 2)

Enthalpies of formation of F₂SO, F₂SO₂, FClSO and FClSO₂ molecules have been determined using ab initio molecular orbital theory and density functional theory (DFT) calculations. Different DFT approaches and levels of the Gaussian-3 and the complete basis set (CBS) ab initio model chemistries have been employed to calculate enthalpies of formation from both total atomization energies and isodesmic reaction schemes. The best values at 298 K for F₂SO, F₂SO₂, FClSO and FClSO₂ as derived from an average of G3, G3B3, CBS-Q and CBS-QB3 isodesmic energies are −140.6, −181.1, −92.6 and −132.3 kcal mol⁻¹, respectively. The results obtained suggest that the accumulated small component errors found in the DFT-based methods are significantly reduced at the ab initio levels employed. Structural properties, harmonic vibrational frequencies, mode assignations and infrared intensities derived from B3LYP and mPW1PW91 functional with the 6-311+G(3df) basis set are presented.     

CH2＝CHCl与O(3P)反应的理论研究

用量子化学密度泛函理论和QCISD (Quadratic configuration interaction calculation)方法, 对O(³P)与CH₂CHCl的反应进行了理论研究. 在UB3LYP/6-311＋＋G(d,p), UB3LYP/6-31＋＋G(3df, 3pd)计算水平上, 优化了反应物、产物、中间体和过渡态的几何构型, 并在UQCISD(T)/6-311＋＋G(2df,2pd)水平上计算了单点能量. 为了确证过渡态的真实性, 在UB3LYP/6-311＋＋G(3df,3pd)水平上进行了内禀坐标(IRC)计算和频率分析, 并确定了反应机理. 研究结果表明, 反应主要产物为CH₂CHO和Cl.     

Ab initio quantum chemical studies on the reactions of CF3O2 with OH

The potential energy surface for the CF₃O₂ + OH reaction has been theoretically investigated using the DFT (B3LYP/6-311G(d,p)) level of theory. Both singlet and triplet potential energy surfaces are investigated. The reaction mechanism on the triplet surface is simple. However, the reaction mechanism on the singlet surface is more complicated. It is revealed that the formation of CF₃O + HO₂ is the dominant channel on the triplet surface. The potential energy surface (PES) for this reaction has been given according to the relative energies calculated at the DFT/B3LYP/6-311G(d,p) level. Because this reaction involves both triplet and singlet states, triplet–singlet intersystem crossing (ISC) crossing also have been investigated in this paper.