Hydrogen Bonding Properties of the Complexes of Formaldehyde and its Derivatives with HF and HCl

 The complexes of formaldehyde and some of its derivatives with HF and HCl were investigated at HF/6-311 + +G^** and MP2/6-311 + +G^** levels of theory. Interaction energies were corrected for the basis set superposition error (BSSE). The full optimizations of dimers and monomers were performed during calculations. The Bader theory of atoms-in-molecules (AIM) was also applied for the localization of bond critical points (BCP) and for the calculation the electron densities and their Laplacians at these points. The relationships between H-bond energy and parameters obtained from calculations were also studied.     

An ab initio Study of the Rotamers and Rotations of Propane-1,3-dial by DFT and SCF Calculations

Summary.  Eight planar rotamers of the enol form of malonaldehyde were considered at the HF (Hartree-Fock) and DFT (density functional theory) levels with 6-311G^** and D95^** (Dunning/Huzinaga full double-ζ) basis sets with the aim to establish the most stable of them and to find the energy barriers of their conversions. The results show that the rotamer with an intramolecular hydrogen bond is the most stable one. High energy barriers were ascertained for the conversions including rotations around a CC double bond. Most of the reactions connected with breaking of the hydrogen bond display strongly asymmetric energy barriers. Their transition states were determined as first-order saddle points because of one imaginary frequency in the IR spectrum related with a negative energy gradient. Received July 6, 2000. Accepted (revised) September 7, 2000     

Ab initio Study of Malonaldehyde Rotamers

Summary.  Malonaldehyde rotamer geometries were optimized using ab initio calculations at the HF level with STO-3G^** and 6-21G^** basis sets. The most stable rotamer is the ω-shaped one with cyclic structure and intramolecular hydrogen bond. The most unstable rotamer is that obtained by rotation of the ω-rotamer around the CO single bond by 180° due to the loss of the additional stabilization contributed by the intramolecular H-bond. The energy barriers separating the different rotamers vary between 13 and 233 kJċmol⁻¹. The structure of the transition states is non-planar with rotation angles varying between 72 and 98°. Received January 18, 1999. Accepted (revised) August 4, 1999     

An ab initio Molecular Orbital Study of the Conformational Properties of all-(Z)-Cyclododeca-1,4,7,10-tetraene

Summary.  Ab initio HF/6-31G^* and MP2/6-31G^*//HF/6-31G^* methods were used to calculate the structure optimization and conformational interconversion pathways for all-(Z )-cyclododeca-1,4,7,10-tetraene. This compound adopts the symmetrical crown (C _4v) conformation. Ring inversion takes place via symmetrical intermediates, such as boat-chair (BC, C _s) and twist (C _2h) conformers and requires about 22.3 kJ · mol⁻¹. The calculated strain energies for BC and twist conformers are 5.9 and 13.5 kJ · mol⁻¹. The results of semiempirical AM1 calculations for structural parameters and relative energies of the important geometries of the title compound are in good agreement with the results of ab initio methods. Received July 9, 2001. Accepted September 26, 2001     

Properties of a Ring Critical Pointas Measures of Intramolecular H-Bond Strength

Summary.  The topological parameters derived from the Bader theory such as the electron density and its Laplacian at the ring critical point (RCP) are analysed here as possible measures of the H-bond stength for intramolecular H-bonds. The parameters of RCP correlate well with the other properties of intramolecular H-bonds which are known as good measures of the H-bond strength. The calculations were performed on two samples of compounds with intramolecular H-bonds: the derivatives of malonaldehyde and the derivatives of o-hydroxybenzaldehyde. MP2 and HF calculations were carried out using a 6-311++G^** basis set. E-mail: slagra@krysia.uni.lodz.pl Received February 18, 2002; accepted (revised) May 27, 2002     

Experimental and Theoretical Studies on (<Emphasis Type="Italic">p</Emphasis>-methoxyphenyl)thiosemicarbazide

The title compound, (p-methoxyphenyl)thiosemicarbazide, has been characterized by elemental analysis, IR, electronic spectroscopy, and single-crystal X-ray diffraction. Ab initio calculations of the structure, atomic charges, natural bond orbital, topological analysis, and thermodynamic functions of the title compound were performed at HF/6-311G^** and B3LYP/6-311G^** levels of theory. The calculated results show that the sulfur atom and nitrogen atoms have bigger negative charges, which result in that they are the potential sites to react with the metallic ions. Electronic absorption spectra were calculated by the time-dependent density functional theory (TD-DFT) and configuration interaction single-excitation (CIS) methods and they are corresponding to the experimental values. The calculation of the second-order optical nonlinearity was carried out, and the molecular hyperpolarizability was 2.592×10⁻³⁰ esu, indicating it is a potential candidate as second-order nonlinear optical material.     

Quantum chemical calculation studies on 4-phenyl-1-(1-phenylethylidene)thiosemicarbazide

Ab initio calculations of the structure, atomic charges, natural bond orbital and thermodynamic functions have been performed at HF/6-311G^** and B3LYP/6-311G^** levels of theory for the title compound of 4-phenyl-1-(1-phenylethylidene) thiosemicarbazide. The calculated results show that the sulfur atom and all of the nitrogen atoms have bigger negative charges and that they are the potential sites to react with the metallic ions, which make the title compound a multidentate ligand. The coordination ability of the sulfur atom and the nitrogen atom of C=N double bond increases with the increase of polarity of the solvent. Electronic absorption spectra have been calculated by time-dependent density functional theory (TD-DFT) method. The calculation of the second-order optical nonlinearity has also been carried out with the PM3 semi-empirical method, resulting in the molecular hyperpolarisability is 5.477×10⁻³⁰ esu.     

A study of methanetetraol dehydration to carbonic acid

Two alternative dehydration reactions C(OH)₄ → (HO)₂CO + H₂O and C(OH)₄ + H₂O → (HO)₂CO + 2H₂O are studied by ab initio Becke3LYP/6–311 + G^** and MP2/6–31G^** methods. Calculated energy and geometry characteristics of intermediates and transition states predict a catalytic effect of one water molecule and the exothermism of the transformations. Relevant HF/6–311 + G^**, HF/6–31G^**, HF/6–31G, and HF/3–21G calculations were performed for comparison. © 1997 John Wiley & Sons, Inc.     

Ab initio Study of Malonaldehyde Rotamers

 Malonaldehyde rotamer geometries were optimized using ab initio calculations at the HF level with STO-3G^** and 6-21G^** basis sets. The most stable rotamer is the ω-shaped one with cyclic structure and intramolecular hydrogen bond. The most unstable rotamer is that obtained by rotation of the ω-rotamer around the CO single bond by 180° due to the loss of the additional stabilization contributed by the intramolecular H-bond. The energy barriers separating the different rotamers vary between 13 and 233 kJċmol⁻¹. The structure of the transition states is non-planar with rotation angles varying between 72 and 98°.     

Ab initio Study of the Keto-Enol Equilibriumof Malonaldehyde

Summary.  The mechanism of the keto-enol tautomerism of malonaldehyde was studied by ab initio methods using 6-21G^** and 6-311G^** basis functions at the HF level. Two separate mechanisms were examined: through-space proton transfer in the ω-shaped form and through-space proton transfer in a sickle-shaped form obtained from the ω form by rotation. The transition state structure of the ω form is non-planar, whereas that of the sickle form is planar. The sickle form is connected with a 2^nd order saddle, indicating that there should exist a lower energy barrier, i.e. that the through-bond mechanism may be preferred. The calculated energy barriers of keto-enol tautomerism for the sickle form is twice as high as those for the omega form. Received January 18, 1999. Accepted (revised) August 4, 1999     

Tautomerism of xanthine: The second-order MØller-Plesset study

Four 9H and four 7H tautomers of DNA base xanthine were studied by the ab initio LCAO-MO method at the MP2/6-311G^**//HF/6-31G^** and MP2/6-31G^**//HF/6-31G^** approximations. All calculated structures are minima at the HF/6-31G^** potential energy surface with the dioxo 7H tautomer (A1) being the global minimum. The second most stable tautomer, dioxo-9H (B1) is by 9 kcal/mol less stable. For the A1 B1 transition the calculated MP2 energy gap corresponds to the equilibrium constant of 2 × 10^–7. Therefore, only the major tautomeric form A1 is predicted to be detectable in the gas phase. The 7H and 9H groups of tautomers are discussed separately. Within both groups, the dioxo form (A1-7H, B1-9H) is the most stable one and is succeeded by the 2-dihydroxy (A2, B2) form. However, while the energy difference between A1 and A2 is 10 kcal/mol, the energy difference between B1 a B2 is only 2 kcal/mol. The effect of polar environment was estimated by the SCRF method, using a spherical cavity, at the HF/6-31G^** level. These calculations did not change the gas phase stability order of the tautomers. However, the energy difference between A1 and B1 decreased from 9 kcal/mol at the HF/6-31G^** level to 4 kcal/mol at the SCRF HF/6-31G^** level.     

Synthesis, structure and quantum chemical calculations on p-trifluoromethylphenyl thioacid amide

The title compound of p-trifluoromethylphenyl thioacid amide has been synthesized in one step and characterized by elemental analysis, UV and X-ray single crystal diffraction. Ab initio calculations indicate that both HF/6-311G^** and B3LYP/6-311G^** methods can reproduce the title compound well. Electronic absorption spectra calculated by the time-dependent density functional theory (TD-DFT) show that the two absorption bands are mainly derived from the contribution of bands π → π^*. Thermodynamic properties of the title compound have been predicted based on the optimized structure. The calculation of the second order optical nonlinearity also has been carried out, and the molecular hyperpolarizability is 2.31770 × 10⁻³⁰ esu.     

Pathways of the reactions of nucleophilic addition of H2O and HF molecules to formaldehyde in the gas phase and in the complex with formic acid:ab initio calculations

The gradient pathways of the reactions of nucleophilic addition of H₂O and HF molecules to formaldehyde in the gas phase and in the XH…H₂CO…HC(O)OH complex (X=OH, F) were calculated by theab initio RHF/6-31G^**, MP2(fc)/6-31G^**, and MP2(full)/6-311++G^** methods. Both reactions proceed concertedly. The formation of H-bonded bimolecular pre-reaction complexes is the initial stage of the gas-phase reactions; at the same time, no indications of the formation of stable π-complexes were found on the potential energy surfaces of systems under study. The calculated energy barriers to the gasphase reactions exceed 40 kcal mol⁻¹, while those to reactions in the complex XH…H₂CO…HC(O)OH (X=OH, F) become more than halved. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2146–2154, November, 1998.     

Ab initio Study of the Keto-Enol Equilibriumof Malonaldehyde

 The mechanism of the keto-enol tautomerism of malonaldehyde was studied by ab initio methods using 6-21G^** and 6-311G^** basis functions at the HF level. Two separate mechanisms were examined: through-space proton transfer in the ω-shaped form and through-space proton transfer in a sickle-shaped form obtained from the ω form by rotation. The transition state structure of the ω form is non-planar, whereas that of the sickle form is planar. The sickle form is connected with a 2^nd order saddle, indicating that there should exist a lower energy barrier, i.e. that the through-bond mechanism may be preferred. The calculated energy barriers of keto-enol tautomerism for the sickle form is twice as high as those for the omega form.     

Structures and stability of N7+ and N7− clusters

Ab initio molecular orbital theory and density functional theory have been used to study nine isomers of N₇ ionic clusters with low spin at the HF/6-31G*, MP2/6-31G*, B3LYP/6-31G*, and B3LYP/6-311(+)G* levels of theory. All stationary points are examined with harmonic vibrational frequency analyses. Four N₇ ⁺ isomers and five N₇ ⁻ isomers are determined to be local minima or very close to the minima on their potential-energy hypersurfaces, respectively. For N₇ ⁺ and N₇ ⁻, the energetically low lying isomers are open-chain structures (C _{2 v} and C _{2 v} or C₂). The results are very similar to those of other known odd-number nitrogen ions, such as N₅ ⁺, N₉ ⁺, and N₉ ⁻, for which the open-chain structures are also the global minima. This research suggests that the N₇ ionic clusters are likely to be stable and to be potential high-energy-density materials if they could be synthesized. Received: 16 July 2001 / Accepted: 8 October 2001 / Published online: 21 January 2002     

Theoretical Study of the Interactions between Isolated <Emphasis Type="Italic">DNA</Emphasis> Bases and Various Groups IA and IIA Metal Ions by <Emphasis Type="Italic">Ab Initio</Emphasis> Calculations

Summary. Interactions of the DNA bases adenine (A), guanine (G), cytosine (C), and thymine (T) with various metal ions (M) of groups IA and IIA of the periodic table of the elements were studied at the HF, MP2, and DFT levels of theory. The structures and thermodynamic stabilities of these species were studied at the gas phase. The calculations uphold that there exist two active sites in G and one in A, C, and T. The calculations also show that the O² atom in T is a more active site for metal ion bindings than that in C. The stability energies for G … M complexes are larger than those for A … M complexes and the stability energies for T … M complexes are larger than those for C … M complexes. As z/r ratio for the metal ion increases, the interaction energy for the complex increases systematically. Thermodynamic quantities such as ΔH, ΔG, ΔS, and ln K were determined for each complexation reaction, [Base+M ⁿ⁺ →(Base … M) ⁿ⁺]. A, G, and C complexation reactions except for C … Rb⁺ are exothermic. The situation is quite different for T complexation reactions and all except for T … Be²⁺ and T … Mg²⁺ are endothermic.     

An ab initio Molecular Orbital Study of the Conformational Properties of all-( Z )-Cyclododeca-1,4,7,10-tetraene

 Ab initio HF/6-31G^* and MP2/6-31G^*//HF/6-31G^* methods were used to calculate the structure optimization and conformational interconversion pathways for all-(Z )-cyclododeca-1,4,7,10-tetraene. This compound adopts the symmetrical crown (C _4v) conformation. Ring inversion takes place via symmetrical intermediates, such as boat-chair (BC, C _s) and twist (C _2h) conformers and requires about 22.3 kJ · mol⁻¹. The calculated strain energies for BC and twist conformers are 5.9 and 13.5 kJ · mol⁻¹. The results of semiempirical AM1 calculations for structural parameters and relative energies of the important geometries of the title compound are in good agreement with the results of ab initio methods.     

Pathways of the reaction of nucleophilic addition of ammonia to formaldehyde in the gas phase and in the complex with formic acid:ab initio calculations

The gradient pathways of the reaction of nucleophilic addition of ammonia to formaldehyde were calculated for free molecules and in the NH₃...H₂CO...HC(O)OH complex by theab initio RHF/6-31G^**, MP2(fc)/6-31G^**, and MP2(full)/6-311++G^** methods. Both reactions proceed concertedly. In the first case, the reaction successively passes through two transitional states with an energy barrier exceeding 35 kcal mol⁻¹. In the case of the complex with formic acid, the reaction follows a conventional pathway, although its activation barrier calculated by the RHF/6-31G^** and MP2(fc)/6-31G^** methods decreases to 12.6 and 3.8 kcal mol⁻¹, respectively. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 13–20, January, 1998.     

Investigation of the effects of ionic hydrogen bonds (COH–C and N–HOC) in crystalline dl-proline by ab initio and DFT calculated NQR parameters

In this paper, we have calculated the nuclear quadrupole resonance (NQR) parameters of the quadrupole nuclei involved in the hydrogen bonds (CO⁻H–C and ⁺N–H⁻OC) in the monomer and pentameric cluster of dl-proline by HF and B3LYP methods and basis sets of 6-311+G^* and 6-311++G^**. These computations are performed on the basis of X-ray diffraction structural data of dl-proline. The results indicate that the calculations including hydrogen-bonding (HB) interactions (in pentamer) are in better agreement with the experimental data than those in which these interactions are neglected (in monomer). The quantum chemical calculations show that the intermolecular hydrogen-bonding interactions play an important role in determination of the NQR parameters of ¹⁴N, ²H of group and ¹⁷O.     

The Keto-Enol Equilibrium of Pentane-2,4-dione Studied by ab initio Methods

Summary.  The mechanism of the keto-enol interconversion of pentane-2,4-dione (trivial name: acetylacetone, acac) was examined at the restricted Hartree-Fock (HF) level and the DFT correlation functional BLYP method using the 6-311G^** basis, both included in the program GAUSSIAN 98. Two initial enol forms are considered: the omega and sickle forms, related by a rotation of 180° around the OC*CC bond. The study is restricted to the through-space transfer of the hydroxyl proton to C(2). The two geometry-optimized enol forms are planar; the geometry optimization of the diketone forms leads to the same non-planar structure, regardless of the starting enol geometry. The transition state of the through-space omega-enol→diketone conversion has also a non-planar structure, indicating that the hydroxyl proton moves outside of the CCC plane. The BLYP-calculated energy barrier of the forward (omega-enol→diketone) conversion is 245 kJ·mol⁻¹, that of the reverse (diketone→omega-enol) conversion 222 kJ·mol⁻¹; thus, an almost symmetric barrier, which is not thermally accessible, is defined. The energy barrier for the sickle-enol→diketone conversion is considerably lower (187 kJ·mol⁻¹), to access the sickle form from the more stable omega form, a rotation is needed (energy barrier: 88 kJ·mol⁻¹). The HF-calculated barriers are 1.3–1.4 times higher than those obtained with the BLYP method. Received July 6, 2000. Accepted (revised) September 8, 2000