Ab initio studies of peroxynitrite anion-water complexes

Quantum mechanical methods have been applied to thecis-ONOO^–-H₂O,cis-ONOO^–-(H₂O)₂ andtrans- ONOO^–-H₂O complexes. Equilibrium geometries, binding energies, net atomic charges and vibrational frequencies are presented for several different arrangements. The MØller-Plessett second-order perturbation (MP2) method predicted shorter hydrogen bonds than the SCF method, but the computed Hartree-Fock (HF) binding energies are similar to counterpoise corrected MP2 values. The geometry changes of ONOO^– and water after solvation are examined. The ONOO^– and H₂O bond length changes follow typical hydrogen bond structural trends, whereas bond angles in ONOO^– are unaffected when the hydrogen bond is formed, similar to the conclusions from NO ₂ ^– -(H₂O) _n HF/6-31G studies and Monte Carlo simulations. Thecis-ONOO^–-(H₂O) _n frequencies are compared with the solution Raman spectrum and with calculations on isolated ONOO^–.     

Ab initio and DFT theory studies of interaction of thymine with formaldehyde

In this article, the interaction of formaldehyde (FA) with thymine is theoretically investigated by computational chemistry methods. The optimization geometries and vibrational frequencies of FA, thymine and three complexes between thymine and FA have been calculated by using the density functional theory and ab initio methods at the B3LYP/6-311G(d, p) and MP2/6-311G(d, p) levels. The NBO and AIM methods are used to analyse interaction as well. Conformers (A), (B) and (C) are cyclic structures with C–H***O and N–H***O hydrogen bonds on a common plane. The corrected complex interaction energies of cyclic structures (A), (B) and (C) at MP2/6-311G(d, p) levels are −38.41, −26.94 and −26.01 kJ/mol, respectively. The order of stability is (A) > (B) > (C).     

Ab initio and DFT studies on hydrolyses of phosphorus halides

Hydrolyses of phosphorus halides, (RO)(2)POX where R = H or Me and X = F or Cl, in the gas phase and in the reaction field have been investigated theoretically with ab initio and the density functional theory (DFT). The free energy of activation in the reaction field was also estimated using the Onsager method with a correction of entropy change and basis set superposition error (BSSE). The reaction of (MeO)(2)POF proceeds through a path with bifunctional catalysis regardless of the medium, but the reaction of (MeO)(2)POCl proceeds through bifunctional and general base catalysis in the gas phase and in water, respectively. The estimated free energy barrier of 23 kcal/mol for the hydrolysis of (MeO)(2)POF is in good agreement with the experimental values of 24 kcal/mol, and relative barrier of 3 kcal/mol to the (MeO)(2)POCl is also in good agreement with the experimental values of 5 kcal/mol of diisopropyl phosphorus halides ((Pr(i)O)(2)POX, X = F and Cl).     

Vibrational frequencies and infrared intensities of the hydrogen-bonded complexes of nitrous acid with ethers: ab initio and DFT studies

The vibrational spectra of the binary complexes formed by HONO-trans and HONO-cis with dimethyl and diethyl ethers have been investigated using ab initio calculations at the SCF and MP2 levels with 6-311++G(d,p) basis set and B3LYP calculations with 6-31G(d,p) and 6-31+G(d,p) basis sets. Full geometry optimisation was made for the complexes studied. The accuracy of the ab initio calculations have been estimated by comparison between the predicted values of the vibrational characteristics (vibrational frequencies and infrared intensities) and the available experimental data. It was established, that the methods, used in this study are well adapted to the problem under examination. The predicted values with the B3LYP calculations are very near to the results, obtained with 6-311++G(d,p)/MP2. The ab initio and DFT calculations show that the changes in the vibrational characteristics (vibrational frequencies and infrared intensities) upon hydrogen bonding for the hydrogen-bonded complex (CH3)2O...HONO-trans are larger than for the complex (CH3)2O...HONO-cis.     

N-甲替甲酰胺-水的氢键团簇的从头计算研究

The N-methylformamide（NMF）-water clusters were studied by ab inito calculations at MP2/6-31+G** and MP2 / 6-311 ++ G（d,p）levels. The equilibrium geometries and the dissociation channels and dissociation energies of both neutral and ionic NMF-H2O clusters are presented. For N-methylformamide,cis-form has lower energy than trans-form. In NMFH+,the proton prefers to link with the O atom of N-methylformamide. The results show that both cis- and trans- form of NMF can form a linear hydrogen bond with water. Although the energy of trans-NMF is higher than cis-NMF,trans-form exits more stably because it can form a double hydrogen bond with water. After the ionization of the NMF-H2O cluster,both the cis- and the trans-form will produce protonated products.     

Ab initio and DFT studies on vibrational spectra of some mixed carbonyl-halide complexes of ruthenium(II)

The vibrational spectra of Ru(CO)6(2+) and some of its mixed carbonyl-halide complexes, cis-Ru(CO)2X4(2-), fac-Ru(CO)3X3- and Ru(CO)5X+ (X = F, Cl, Br and I), have been systematically investigated by ab initio RHF and density functional B3LYP methods with LanL2DZ and SDD basis sets. The calculated vibrational frequencies of complexes Ru(CO)6(2+), cis-Ru(CO)2X4(2-) and fac-Ru(CO)3X3- are evaluated via comparison with the experimental values. In the infrared frequency region, the C-O stretching vibrational frequencies calculated at B3LYP level with two basis sets are in good agreement with the observed values with deviations less than 5%. In the far-infrared region, the B3LYP/SDD method achieved the best results with deviations less than 8% for Ru-X stretching and less than 2% for Ru-C stretching vibrational frequencies. The vibrational frequencies for Ru(CO)5X+ that have not been experimentally reported were predicted.     

Ab initio/DFT and AIM studies on dual hydrogen-bonded complexes of 2-hydroxypyridine/2-pyridone tautomerism

The second-order M?ller-Plesset (MP2) and density functional theory (DFT) calculations have been carried out to investigate the structures and stabilities of hydrogen (H-) bonded 2-hydroxypyridine (2HP)/2-pyridone (2PY) dimeric forms as well as 2HP-2PY complexes. The results on single-point counterpoise (CP) correction of these complexes were compared against CP-optimized correction. The nature of the intermolecular contacts in the sense of normal H-bond or blue-shifting H-bond was determined on the basis of harmonic vibrational, atom-in-molecule (AIM), and natural bond orbital (NBO) analysis. A blue-shifting C-H...N H-bond was found and NBO analysis revealed a slight decrease in the population of the contacting sigmaC-H* antibonding orbital as the primary reason of the C-H contraction. Good correlations have been established between the interaction energies and the H-bond distances versus other characteristic H-bond parameters.     

Ab initio and DFT studies of the vibrational spectra of hydrogen-bonded PhOH...(H2O)4 complexes

The vibrational characteristics (vibrational frequencies and infrared intensities) for the hydrogen-bonded complex of phenol with four water molecules PhOH...(H2O)4 (structure 4A) have been predicted using ab initio and DFT (B3LYP) calculations with 6-31G(d,p) basis set. The changes in the vibrational characteristics from free monomers to a complex have been calculated. The ab initio and B3LYP calculations show that the observed four intense bands at 3299, 3341, 3386 and 3430 cm(-1) can be assigned to the hydrogen-bonded OH stretching vibrations in the complex PhOH...(H2O)4 (4A). The complexation leads to very large red shifts of these vibrations and very strong increase in their IR intensity. The predicted red shifts for these vibrations with B3LYP/6-31G(d,p) calculations are in very good agreement with the experimentally observed. It was established that the phenolic OH stretching vibration is the most sensitive to the hydrogen bonding. The predicted red-shift with the B3LYP/6-31G(d,p) calculations for the most stable ring structure 4A (-590 cm(-1)) is in better agreement with the experimentally observed than the red-shift, predicted with SCF/6-31G(d,p) calculations. The magnitude of the wavenumber shift is indicative of relatively strong OH...H hydrogen-bonded interaction. The complexation between phenol and four water molecules leads to strong increase of the IR intensity of the phenolic OH stretching vibration (up to 38 times).     

Ab initio DFT investigations on structure of copper(I) bis-diazine complexes

Supramolecular self-assembling processes of nitrogen bidendated heterocycles are fundamental for the understanding of rules which predestine to their spontaneous formation. In our approach ab initio DFT method has been used to resolve six Cu(I) complexes. The collected data show that only four structures converged into a quasi-tetrahedral [L₂Cu][BF₄] geometry. A special feature in case of the [(bpy–bpz)₂Cu][BF₄] hetero-complex, not observed in case of the corresponding Cu(I) homo-complexes, is the increased participation of p orbitals of the Cu⁺ to the HOMO.     

Ab initio and DFT studies of hydrogen bond interactions in difluoroacetic acid dimer

Density functional theory (DFT) and ab initio calculations were performed for difluoroacetic acid (DFA). Eight theoretically possible conformers were considered and by using conformational analysis only three stable conformers were found. The hydrogen bonding interaction of DFA complex has been investigated using DFT and ab initio methods for cis conformers. Stabilization energies of dimers including basis set superposition error and ZPE were found in the range 8.89–13.08 kcal mol⁻¹. It was found that EFC dimer is slightly more stable. Red shift of O–H bond in the range −226.3 to 505.7 cm⁻¹ predicted for dimers. The natural bond orbital analysis was applied to characterize nature of the interaction.     

Ab initio studies of

Ab initio calculations of the [1,5]-H shift in (3Z)-penta-1,3-diene and other substituted pentadienes and heteroanalogues using the hybrid density functional Becke3LYP with the 6-31G basis set are presented. Electron-donating substituents, such as methoxy in (3Z)-3-methoxypenta-1,3-diene 1, or heteroatoms such as a nitrogen atom in (Z)-ethylidenevinylamine 2, (1Z)-buta-1,3-dienylamine 3, (2Z)-but-2-enylideneamine 4, (Z)-allylidenemethylamine 5, and methylene-(Z)-propenylamine 6 are introduced. The electron-withdrawing fluoride is substituted for the hydrogen atoms in (3Z)-3-fluoropenta-1,3-diene 7, (3Z)-2,4-difluoropenta-1,3-diene 8, (3Z)-1,1',2,3,4,5,5'-heptafluoropenta- 1,3-diene 10, (1E,3E)-1,3,5-trifluoropenta-1,3-diene 11, and (1Z,3E)-1,3,5- trifluoropenta-1,3-diene 13. A detailed analysis of the geometries, energies, and electronic characteristics of the sigmatropic transposition compared to those of the unsubstituted case provides insights into substituent effects of this prototype of pericyclic reaction. The inductive and mesomeric effects of heteroatoms or heterosubstituents are of a great importance and in a continuous balance in the energetics of the transformation. Sterics can also play an important role due to the geometrical constraints of the reaction. As a general trend, decreasing the electron density of the phi system destabilizes the aromatic transition structure and increases the activation energy, and vice versa.     

Comparative study of the hydrogen-bonded complexes of phenol and o-cyanophenol with CO Ab initio and DFT approachs

The structures, stability and vibrational spectra of the hydrogen-bonded complexes of carbon monoxide (CO) with phenol and o-cyanophenol (syn and anti) have been studied using ab initio and DFT calculations. Full geometry optimization has been performed for the studied complexes by DFT (BLYP/6-311++G(d,p)) calculations. The calculations show that the hydrogen-bond formation of carbon monoxide (CO) with phenol and o-cyanophenol (syn and anti) leads to the following stable structures: C6H5OH...CO (1A); C6H5OH...OC (1B); (syn) o-CNC6H4OH...CO (2A-syn); (syn) o-CNC6H4OH...OC (2B-syn); (anti) o-CNC6H4 OH...CO (2A-anti) and (anti) o-CNC6H4OH...OC (2B-anti). Having in mind the corrected values of the dissociation energy, the studied hydrogen-bonded complexes can be ordered according their stability as follows: 2A-anti>2A-syn>1A>2B-anti>1B>2B-syn. The predicted red-shifts for the nuOH vibration with the B3LYP/6-311++G(d,p) calculations for the structures 1A (-46 cm-1), 2A-syn (-60 cm-1) and 2A-anti (-73 cm-1) are in very good agreement with the experimentally observed. The magnitudes of the wavenumber shifts are indicative of relatively weak OH...C hydrogen-bonded interactions. The calculations predict an increase of the IR intensity of the nuOH vibration in the complexes 1A, 2A-anti and 2A-syn up to five times.     

Ab initio and DFT studies on van der Waals trimers: the OCS.(CO2)2 complexes

Ab initio calculations [MP2, MP4SDTQ, and QCISD(T)] using different basis sets [6-31G(d,p), cc-pVXZ (X = D, T, Q), and aug-cc-pVDZ] and density functional theory [B3LYP/6-31G(d,p)] calculations were carried out to study the OCS.(CO2)2 van der Waals trimer. The DFT has proved inappropriate to the study of this type of systems where the dispersion forces are expected to play a relevant role. Three minima isomers (two noncyclic and one cyclic) were located and characterized. The most stable isomer exhibits a noncyclic barrel-like structure whose bond lengths, angles, rotational constants, and dipole moment agree quite well with the corresponding experimental values of the only structure observed in recent microwave spectroscopic studies. The energetic proximity of the three isomers, with stabilization energies of 1442, 1371, and 1307 cm-1, respectively, at the CBS-MP2/cc-pVXZ (X = D, T, Q) level, strongly suggests that the two unobserved structures should also be detected as in the case of the (CO2)3 trimer where both noncyclic and cyclic isomers have been reported to exist. The many-body symmetry-adapted perturbation theory is employed to analyze the nature of the interactions leading to the formation of the different structures. The three-body contributions are small and stabilizing for the two most stable structures and almost negligible for the cyclic isomer.     

Ab initio and DFT studies on tautomerism of indazole in gaseous and aqueous phases

Electronic structure of optimized Ge₅, Ge₁₇, Ge₅–O and Ge₅ embedded in SiO₂ nanoparticles have been studied by density functional theory to find out the effect of cluster size and Ge–O bond(s) on the optical energy gap between LUMO and HOMO. It was found that the optical energy gap depends on both cluster size and the number of Ge–O bonds nonlinearly. The optical energy gap was found to be in visible light range when the Ge₅ nanoparticle has been embedded in SiO₂ matrix.     

Ab initio and DFT studies of the molecular structures and vibrational spectra of succinonitrile

The Molecular structure, conformational stability and vibrational frequencies of succinonitrile NCCH2CH2CN have been investigated with ab initio and density functional theory (DFT) methods implementing the standard 6-311++G* basis set. The potential energy surfaces (PES) have been explored at DFT-B3LYP, HF and MP2 levels of theory. In agreements with previous experimental results, the molecule was predicted to exist in equilibrium mixture of trans and gauche conforms with the trans form being slightly lower in energy. The vibrational frequencies and the corresponding vibrational assignments of succinonitrile in both C2h and C2 symmetry were examined theoretically and the calculated Infrared and Raman spectra of the molecule were plotted. Observed frequencies for normal modes were compared with those calculated from normal mode coordinate analysis carried out on the basis of ab initio and DFT force fields using the standard 6-311++G* basis set of the theoretical optimized geometry. Theoretical IR intensities and Raman activities are reported.     

Hydrogen-bonded complexes of serotonin with methanol and ethanol: a DFT study

Density functional theoretical studies on hydrogen-bonded complexes of serotonin with methanol/ethanol have been carried out in a systematic way. The conformational analysis led to ten stable conformers that can be either gauche or anti depending on the dihedral angle values taken by ethylamine side chain and the 5-hydroxyl group. Serotonin-molecules strongly bind with ethanol than methanol. Ethylamine side chain is the most reactive site in both methanol/ethanol complexes and it is responsible for the stability order. The topological parameters, electron density, and Laplacian of electron density show excellent correlation with the hydrogen bond length. Natural bond orbital analysis confirms C–H···O hydrogen bond formed between the serotonin–alcohol complexes to be red shift in nature except for Gph(out)anti complex both with methanol and ethanol to be blue shifted. The energy decomposition analysis reveals that strong interactions between serotonin and ethanol/methanol are due to the attractive contributions from the electrostatic component.     

Ab initio and DFT studies on vibrational spectra of some halides of group IIIB elements

The vibrational spectra of some group IIIB elements halides MX(3) and their dimmers, M(2)X(6) (M=Sc(III), Y(III), La(III); X=F, Cl, Br, I), have been systematically investigated by ab initio restricted Hartree-Fock (RHF) and density functional B3LYP methods with LanL2DZ and SDD basis sets. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. The vibrational frequencies, calculated by two methods with different basis sets, are compared to each other. The effect of the methods and the basis sets used on the calculated vibrational frequencies are discussed. Some vibrational frequencies of these complexes are also predicted.     

Ab initio studies on the zero-field splitting parameters of manganese porphyrin complexes

The magnetic property of a one-dimensional magnetic chain, 5,10,15,20-tetrakis(4-bromophenyl)porphyrinatomanganese(III) tetracyanoethenide ([MnTBrPP]⁺[TCNE]⁻), is investigated by using model complexes and ab initio calculations. In these models, MnTBrPP is reduced to a manganese porphyrin complex (MnP). The spin-polarized density functional theory (UDFT) and the hybrid UDFT were used to calculate the complexes, and Pederson’s scheme was used to calculate their zero-field splitting (ZFS) parameters. We found from the model calculations that the TCNE coordination hardly affects the magnetic anisotropy of MnP.     

Ab initio studies on calicene

Optimum geometries of planar and 90°-twisted C_2v calicene are calculated with single-configuration STO-3G and 3-21-G wavefunctions. The barrier to ring–ring rotation is computed. Bond alternation is pronounced in the planar form and decreases in the twisted form, while dipolar character increases on twisting.