A theoretical investigation on the proton transfer tautomerization mechanisms of 2-thioxanthine within microsolvent and long range solvent

A relative complete study on the mechanisms of the proton transfer reactions of 2-thioxanthine was carried out with density functional theory. The models were designed with monohydrated and dihydrated microsolvent catalyses either with or without the presence of water solvent considered with the polarized continuum model (PCM). A total number of 114 complexes and 67 transition states were found with the B3LYP/6-311+G** calculations. The energies were refined with both B3LYP/aug-cc-pVTZ and PCM-B3LYP/aug-cc-pVTZ methods. The activation energies were reported with respect to the Gibbs free energies obtained in conjunction with the standard statistical thermodynamics. Possible reaction pathways were confirmed with the intrinsic reaction coordinates. Pathways via C8 atom on the imidazole ring, via the bridged C4 and C5 atoms between pyrimidine and imidazole rings and via N, O and S atom on the pyrimidine ring were examined. The results show that the most feasible pathway is the proton transfers within the long range solvent surrounding via the N, O and S atoms in the pyrimidine ring with di-hydrated catalysis: N(7)H?+?2H₂O?→?IM89?→?IM90?→?P13?+?2H₂O?→?IM91?→?IM92?→?P6?+?2H₂O?→?IM71?→?IM72?→?P7?+?2H₂O?→?IM107?→?IM108?→?P18?+?2H₂O?→?IM111?→?IM112?→?P19?+?2H₂O?→?IM113?→?IM114?→?P17?+?2H₂O?→?IM105?→?IM106?→?N(9)H?+?2H₂O that has the highest energy barrier of 44.0 kJ mol^?1 in the transition of IM89 to IM90 via TS54. The small energy barrier is in good agreement with the experimental observation that 2-TX tautomerizes at room temperature in water. In the aqueous phase, the most stable intermediate is found to be IM21 [N(7)H?+?2H₂O] and the possible co-existing species are the monohydrated IM1, IM9, IM39 and IM46, and the di-hydrated IM5, IM8, IM13, IM16, IM81, IM89, IM90, IM91 and IM106 complexes that have a relative concentration larger than 10^?6 (1 ppm) with respect to IM21.

A B3LYP and MP2(full) theoretical investigation into the strength of the C-NO2 bond upon the formation of the molecule-cation interaction between Na+ and the nitro group of nitrotriazole or its methyl derivatives

The changes of bond dissociation energy (BDE) in the C–NO₂ bond and nitro group charge upon the formation of the molecule-cation interaction between Na⁺ and the nitro group of 14 kinds of nitrotriazoles or methyl derivatives were investigated using the B3LYP and MP2(full) methods with the 6-311++G**, 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. The strength of the C–NO₂ bond was enhanced in comparison with that in the isolated nitrotriazole molecule upon the formation of molecule-cation interaction. The increment of the C–NO₂ bond dissociation energy (ΔBDE) correlated well with the molecule-cation interaction energy. Electron density shifts analysis showed that the electron density shifted toward the C-NO₂ bond upon complex formation, leading to the strengthened C-NO₂ bond and the possibly reduced explosive sensitivity.

A B3LYP and MP2(full) theoretical investigation into the strength of the C–NO2 bond upon the formation of the intermolecular hydrogen-bonding interaction between HF and the nitro group of nitrotriazole or its methyl derivatives

The changes of bond dissociation energy (BDE) in the C–NO₂ bond and nitro group charge upon the formation of the intermolecular hydrogen-bonding interaction between HF and the nitro group of 14 kinds of nitrotriazoles or methyl derivatives were investigated using the B3LYP and MP2(full) methods with the 6-311++G**, 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. The strength of the C–NO₂ bond was enhanced and the charge of nitro group turned more negative in complex in comparison with those in isolated nitrotriazole molecule. The increment of the C–NO₂ bond dissociation energies correlated well with the intermolecular H-bonding interaction energies. Electron density shifts analyses showed that the electron density shifted toward the C–NO₂ bond upon complex formation, leading to the strengthened C–NO₂ bond and the possibly reduced explosive sensitivity.

A B3LYP and MP2(full) theoretical investigation into the cooperativity effect between dihydrogen-bonding and H–M∙∙∙π (M = Li, Na, K) interactions among HF, MH with the π-electron donor C2H2, C2H4 or C6H6

The DFT-B3LYP/6-311++G(3df,2p) and MP2(full)/6-311++G(3df,2p) calculations were carried out on the binary complex formed by HM (M?=?Li, Na, K) and HF or the π-electron donor (C₂H₂, C₂H₄, C₆H₆), as well as the ternary system FH???HM???C₂H₂/C₂H₄/C₆H₆. The cooperativity effect between the dihydrogen-bonding and H–M???π interactions was investigated. The result shows that the equilibrium distances R _H???H and R _M???π in the ternary complex decrease and both the H???H and H–M???π interactions are strengthened when compared to the corresponding binary complex. The cooperativity effect of the dihydrogen bond on the H–M???π interaction is more pronounced than that of the M???π bond on the H???H interaction. Furthermore, the values of cooperativity effect follow the order of FH???HNa???π?>?FH???HLi???π?>?FH???HK???π and FH???HM???C₆H₆?>?FH???HM???C₂H₄?>?FH???HM???C₂H₂. The nature of the cooperativity effect was revealed by the analyses of the charge of the hydrogen atoms in H???H moiety, atom in molecule (AIM) and electron density shifts methods.

Enhancing and modulating the intrinsic acidity of imidazole and pyrazole through beryllium bonds

The structure and electronic properties of the complexes formed by the interaction of imidazole and pyrazole with different BeXH(BeX₂) (X = H, Me, F, Cl) derivatives have been investigated via B3LYP/6?311+G(3df,2p)//B3LYP/6?31+G(d,p) calculations. The formation of these azole:BeXH(BeX₂) complexes is accompanied by a dramatic enhancement of the intrinsic acidity of the azole, as the deprotonated azole is much more stable after the aforementioned interaction. Most importantly, the increase in acidity is so large that the azole:BeXH or azole:BeX₂ complexes behave as NH acids, which are stronger than typical oxyacids such as phosphoric acid and oxalic acid. Interestingly, the increase in acidity can be tuned through appropriate selection of the substituents attached to the Be atom, permitting us to modulate the electron-accepting ability of the BeXH or BeX₂ molecule.

DFT and docking studies of rhodostreptomycins A and B and their interactions with solvated/nonsolvated Mg2+ and Ca2+ ions

The interactions of L-aminoglucosidic stereoisomers such as rhodostreptomycins A (Rho A) and B (Rho B) with cations (Mg²⁺, Ca²⁺, and H⁺) were studied by a quantum mechanical method that utilized DFT with B3LYP/6-311G**. Docking studies were also carried out in order to explore the surface recognition properties of L-aminoglucoside with respect to Mg²⁺ and Ca²⁺ ions under solvated and nonsolvated conditions. Although both of the stereoisomers possess similar physicochemical/antibiotic properties against Helicobacter pylori, the thermochemical values for these complexes showed that its high affinity for Mg²⁺ cations caused the hydration of Rho B. According to the results of the calculations, for Rho A–Ca²⁺(H₂O)₆, ΔH = ?72.21 kcal?mol^?1; for Rho B–Ca²⁺(H₂O)₆, ΔH = ?72.53 kcal?mol^?1; for Rho A–Mg²⁺(H₂O)₆, ΔH = ?72.99  kcal?mol^?1 and for Rho B–Mg²⁺(H₂O)₆, ΔH = ?95.00  kcal?mol^?1, confirming that Rho B binds most strongly with hydrated Mg²⁺, considering the energy associated with this binding process. This result suggests that Rho B forms a more stable complex than its isomer does with magnesium ion. Docking results show that both of these rhodostreptomycin molecules bind to solvated Ca²⁺ or Mg²⁺ through hydrogen bonding. Finally, Rho B is more stable than Rho A when protonation occurs.

Modulating weak intramolecular interactions through the formation of beryllium bonds: complexes between squaric acid and BeH2

The electronic structure of the two most stable isomers of squaric acid and their complexes with BeH₂ were investigated at the B3LYP/6-311?+?G(3df,2p)// B3LYP/6-31?+?G(d,p) level of theory. Squaric acid forms rather strong beryllium bonds with BeH₂, with binding energies of the order of 60 kJ?mol^?1. The preferential sites for BeH₂ attachment are the carbonyl oxygen atoms, but the global minima of the potential energy surfaces of both EZ and ZZ isomers are extra-stabilized through the formation of a BeH···HO dihydrogen bond. More importantly, analysis of the electron density of these complexes shows the existence of significant cooperative effects between the beryllium bond and the dihydrogen bond, with both becoming significantly reinforced. The charge transfer involved in the formation of the beryllium bond induces a significant electron density redistribution within the squaric acid subunit, affecting not only the carbonyl group interacting with the BeH₂ moiety but significantly increasing the electron delocalization within the four membered ring. Accordingly the intrinsic properties of squaric acid become perturbed, as reflected in its ability to self-associate.

Theoretical investigation on the structure and thermodynamic properties of the 2,4-dinitroimidazole complex with methanol

The structure and thermodynamic properties of the 2, 4-dinitroimidazole complex with methanol were investigated using the B3LYP and MP2(full) methods with the 6-31++G(2d,p) and 6-311++G(3df,2p) basis sets. Four types of hydrogen bonds [N–H?O, C–H?O, O–H?O (nitro oxygen) and O–H?π] were found. The hydrogen-bonded complex having the highest binding energy had a N–H?O hydrogen bond. Analyses of natural bond orbital (NBO) and atoms-in-molecules (AIM) revealed the nature of the intermolecular hydrogen-binding interaction. The changes in thermodynamic properties from monomers to complexes with temperatures ranging from 200.0 to 800.0 K were investigated using the statistical thermodynamic method. Hydrogen-bonded complexes of 2,4-dinitroimidazole with methanol are fostered by low temperatures.

DFT studies of the conversion of four mesylate esters during reaction with ammonia

The energetics of the Menshutkin-like reaction between four mesylate derivatives and ammonia have been computed using B3LYP functional with the 6-31+G** basis set. Additionally, MPW1K/6-31+G** level calculations were carried out to estimate activation barrier heights in the gas phase. Solvent effect corrections were computed using PCM/B3LYP/6-31+G** level. The conversion of the reactant complexes into ion pairs is accompanied by a strong energy decrease in the gas phase and in all solvents. The ion pairs are stabilized with two strong hydrogen bonds in the gas phase. The bifurcation at C2 causes a significant activation barrier increase. Also, bifurcation at C5 leads to noticeable barrier height differentiation. Both B3LYP/6-31+G** and MPW1K/6-31+G** activation barriers suggest the reaction 2 (2a?+?NH₃) to be the fastest in the gas phase. The reaction 4 is the slowest one in all environments.

Modeling the effect of H-bonding interactions and molecular packing on the molecular structure of [Ag(ethylnicotinate)2]NO3 complex

The gas phase molecular structure of a single isolated molecule of [Ag(Etnic)₂NO₃];1 where Etnic = Ethylnicotinate was calculated using B3LYP method. The H-bonding interaction between 1 with one (complex 2) and two (complex 3) water molecules together with the dimeric formula [Ag(Etnic)₂NO₃]₂;4 and the tetrameric formula [Ag(Etnic)₂NO₃]₄;5 were calculated using the same level of theory to model the effect of intermolecular interactions and molecular packing on the molecular structure of the titled complex. The H-bond dissociation energies of complexes 2 and 3 were calculated to be in the range of 12.220–14.253 and 30.106–31.055 kcal?mol^?1, respectively, indicating the formation of relatively strong H-bonds between 1 and water molecules. The calculations predict bidentate nitrate ligand in the case of 1 and 2, leading to distorted tetrahedral geometry around the silver ion with longer Ag–O distances in case of 2 compared to 1, while 3 has a unidentate nitrate ligand leading to a distorted trigonal planar geometry. The packing of two [Ag(Etnic)₂NO₃] complex units; 4 does not affect the molecular geometry around Ag(I) ion compared to 1. In the case of 5, the two asymmetric units of the formula [Ag(Etnic)₂NO₃] differ in the bonding mode of the nitrate group, where the geometry around the silver ion is distorted tetrahedral in one unit and trigonal planar in the other. The calculations predicted almost no change in the charge densities at the different atomic sites except at the sites involved in the C–H?O interactions as well as at the coordinated nitrogen of the pyridine ring.

Microsolvation of Mg2+, Ca2+: strong influence of formal charges in hydrogen bond networks

A stochastic exploration of the quantum conformational spaces in the microsolvation of divalent cations with explicit consideration of up to six solvent molecules [Mg (H ₂ O) _n )]²⁺, (n?=?3, 4, 5, 6) at the B3LYP, MP2, CCSD(T) levels is presented. We find several cases in which the formal charge in Mg²⁺ causes dissociation of water molecules in the first solvation shell, leaving a hydroxide ion available to interact with the central cation, the released proton being transferred to outer solvation shells in a Grotthus type mechanism; this particular finding sheds light on the capacity of Mg²⁺ to promote formation of hydroxide anions, a process necessary to regulate proton transfer in enzymes with exonuclease activity. Two distinct types of hydrogen bonds, scattered over a wide range of distances (1.35–2.15 Å) were identified. We find that in inner solvation shells, where hydrogen bond networks are severely disturbed, most of the interaction energies come from electrostatic and polarization+charge transfer, while in outer solvation shells the situation approximates that of pure water clusters.

Structural characterization of the (MeSH)4 potential energy surface

A random walk on the PES for (MeSH)₄ clusters produced 50 structural isomers held together by hydrogen-bonding networks according to calculations performed at the B3LYP/6–311++G** and MP2/6–311++G** levels. The geometric motifs observed are somewhat similar to those encountered for the methanol tetramer, but the interactions responsible for cluster stabilization are quite different in origin. Cluster stabilization is not related to the number of hydrogen bonds. Two distinct, well-defined types of hydrogen bonds scattered over a wide range of distances are predicted.

Density functional theory investigation of electrophilic addition reaction of bromine to tricyclo[4.2.2.22,5]dodeca-1,5-diene1

The geometry and the electronic structure of tricyclo[4.2.2.2^2,5]dodeca-1,5-diene (TCDD) molecule were investigated by DFT/B3LYP and /B3PW91 methods using the 6-311G(d,p) and 6-311++G(d,p) basis sets. The double bonds of TCDD molecule are syn-pyramidalized. The structure of π-orbitals and their mutual interactions for TCDD molecule were investigated. Potential energy surface (PES) of the TCDD-Br₂ system was studied by B3LYP/6-311++G(d,p) method and the configurations [molecular charge-transfer (CT) complex, transition states (TS1 and TS2), intermediate (INT) and product (P)] corresponding to the stationary points (minima or saddle points) were determined. Initially, a molecular CT-complex forms between Br₂ and TCDD. With a barrier of 22.336 kcal mol^-1 the CT-complex can be activated to an intermediate (INT) with energy 15.154 kcal mol^-1 higher than that of the CT-complex. The intermediate (INT) then transforms easily (barrier 5.442 kcal mol^-1) into the final, N-type product. The total bromination is slightly exothermic. Accompanying the breaking of Br-Br bond, C1-Br, C5-Br and C2-C6 bonds are formed, and C1 = C2 and C5 = C6 double bonds transform into single bonds. The direction of the reaction is determined by the direction of intramolecular skeletal rearrangement that is realized by the formation of C2-C6 bond.

Electron correlation effects and density analysis of the first-order hyperpolarizability of neutral guanine tautomers

Dipole moments (μ), charge distributions, and static electronic first-order hyperpolarizabilities (β _μ ) of the two lowest-energy keto tautomers of guanine (7H and 9H) were determined in the gas phase using Hartree–Fock, Møller–Plesset perturbation theory (MP2 and MP4), and DFT (PBE1PBE, B97-1, B3LYP, CAM-B3LYP) methods with Dunning’s correlation-consistent aug-cc-pVDZ and d-aug-cc-pVDZ basis sets. The most stable isomer 7H exhibits a μ value smaller than that of the 9H form by a factor of ca. 3.5. The β _μ value of the 9H tautomer is strongly dependent on the computational method employed, as it dramatically influences the β _μ (9H)/β _μ (7H) ratio, which at the highest correlated MP4/aug-cc-pVDZ level is predicted to be ca. 5. The Coulomb-attenuating hybrid exchange-correlation CAM-B3LYP method is superior to the conventional PBE1PBE, B3LYP, and B97-1 functionals in predicting the β _μ values. Differences between the largest diagonal hyperpolarizability components were clarified through hyperpolarizability density analyses. Dipole moment and first-order hyperpolarizability are molecular properties that are potentially useful for distinguishing the 7H from the 9H tautomer.

Computational and experimental studies of the electronic excitation spectra of EDTA and DTPA substituted tetraphenylporphyrins and their Lu complexes

Ethylendiaminetetraacetic acid (EDTA) substituted and diethylenetriaminopentaacetic acid (DTPA) substituted aminated free-base tetraphenylporphyrins (H₂ATPP) and the corresponding lutetium(III) complexes have been studied computationally at the density functional theory (DFT) and second-order algebraic diagrammatic construction (ADC(2)) levels using triple-ξ basis sets augmented with polarization functions. The molecular structures were optimized using Becke's three-parameter hybrid functional (B3LYP). The electronic excitation spectra in the range of 400–700 nm were calculated using the ADC(2) and the linear-response time-dependent DFT methods. The calculated spectra are compared to those measured in ethanol solution. The calculated excitation energies agree well with those deduced from the experimental spectra. The excitation energies for the Q_x band calculated at the B3LYP and ADC(2) level are 0.20-0.25 eV larger than the experimental values. The excitation energies for the Q_y band calculated at the B3LYP level are 0.10-0.20 eV smaller than the ADC(2) ones and are thus in good agreement with experiment. The calculated excitation energies corresponding to the B_x and B_y bands are 0.10-0.30 eV larger than the experimental values. The excitation energies of the B_x and B_y bands calculated at the B3LYP level are in somewhat better agreement with experiment than the ADC(2) ones. The calculated and measured band strengths largely agree.

Spin-flip reactions of Zr + C2H6 researched by relativistic density functional theory

Density functional theory (DFT) with relativistic corrections of zero-order regular approximation (ZORA) has been applied to explore the reaction mechanisms of ethane dehydrogenation by Zr atom with triplet and singlet spin-states. Among the complicated minimum energy reaction path, the available states involves three transition states (TS), and four stationary states (1) to (4) and one intersystem crossing with spin-flip (marked by ?): ³ Zr + C ₂ H ₆ → ³ Zr-CH ₃ -CH ₃ ( ³ 1) → ³ TS _1/2 → ³ ZrH-CH ₂ -CH ₃ ( ³ 2) → ³ TS _2/3 ? ¹ ZrH₂-CH₂ = CH₂ ( ¹ 3) → ¹ TS _3/4 → ¹ ZrH ₃ -CH = CH ₂ ( ¹ 4). The minimum energy crossing point is determined with the help of the DFT fractional-occupation-number (FON) approach. The spin inversion leads the reaction pathway transferring from the triplet potential energy surface (PES) to the singlet’s accompanying with the activation of the second C-H bond. The overall reaction is calculated to be exothermic by about 231 kJ mol^?1. Frequency and NBO analysis are also applied to confirm with the experimental observed data.

DFT model cluster studies of O2 adsorption on hydrogenated titania sub-nanoparticles

In the present paper, we examine the general applicability of different TiO₂ model clusters to study of local chemical events on TiO₂ sub-nanoparticles. Our previous DFT study of TiO₂ activation through H adsorption and following deactivation by O₂ adsorption using small amorphous Ti₈O₁₆ cluster were complemented by examination of rutile-type and spherical Ti₁₅O₃₀ nanoclusters. The obtained results were thoroughly compared with experimental data and results of related computational studies using other TiO₂ models including periodic structures. It turned out that all considered model TiO₂ model systems provide qualitatively similar results. It was shown that atomic hydrogen is adsorbed with negligible activation energy on surface O atoms, which is accompanied by the appearance of reduced Ti³⁺ species and corresponding localized band gap 3d-Ti states. Oxygen molecule is adsorbed on Ti³⁺ sites spontaneously forming molecular O₂ ^– species by capturing an extra electron of Ti³⁺ ion, which results in disappearance of Ti³⁺ species and corresponding band gap states. Calculated g-tensor values of Ti³⁺ and O₂ ^– species agree well with the results of EPR studies and do not depend on the used TiO₂ model cluster. Additionally, it was shown that the various cluster calculations provide results comparable with the calculations of periodic structures with respect to the modeling of chemical processes under study. As a whole, the present study approves the validity of molecular cluster approach to study of local chemical events on TiO₂ sub-nanoparticles.

Microsolvation and hydration enthalpies of CaC2O4(H2O) n (n = 0-16) and C2O4 2-(H2O) n (n = 0-14): an ab initio study

We studied hydrated calcium oxalate and its ions at the restricted Hartree–Fock RHF/6-31G* level of theory. Performing a configurational search seems to improve the fit of the HF/6-31G* level to experimental data. The first solvation shell of calcium oxalate contains 13 water molecules, while the first solvation shell of oxalate ion is formed by 14 water molecules. The first solvation shell of Ca(II) is formed by six water molecules, while the second shell contains five. At 298.15 K, we estimate the asymptotic limits (infinite dilution) of the total standard enthalpies of hydration for Ca(II), oxalate ion and calcium oxalate as ?480.78, –302.78 and –312.73 kcal mol^?1, resp. The dissociation of hydrated calcium oxalate is an endothermic process with an asymptotic limit of +470.84 kcal mol^?1.

A theoretical investigation into the cooperativity effect between the H∙∙∙O and H∙∙∙F– interactions and electrostatic potential upon 1:2 (F–:N-(Hydroxymethyl)acetamide) ternary-system formation

The cooperativity effects between the O/N–H???F^– anionic hydrogen-bonding and O/N–H???O hydrogen-bonding interactions and electrostatic potentials in the 1:2 (F^–:N-(Hydroxymethyl)acetamide (signed as “ha”)) ternary systems are investigated at the B3LYP/6-311++G** and MP2/6-311++G** levels. A comparison of the cooperativity effect in the “F^–???ha???ha” and “FH???ha^–???ha” systems is also carried out. The result shows that the increase of the H???O interaction energy in the O–H???O–H, N–H???O–H or N–H???O?=?C link is more notable than that in the O–H???O?=?C contact upon ternary-system formation. The cooperativity effect is found in the complex formed by the O/N–H???F^– and O/N–H???O interactions, while the anti-cooperativity effect is present in the system with only the O/N–H???F^– H-bond or the “FH???ha^–???ha” complex by the N^–???H–F contact. Atoms in molecules (AIM) analysis and shift of electron density confirm the existence of cooperativity. The most negative surface electrostatic potential (V _S,min ) correlates well with the interaction energy E′ _{int.(ha???F–)} and synergetic energy E _syn., respectively. The relationship between the change of V _S,min (i.e., ΔV _S,min ) and E _syn. is also found.