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.     

Perturbative corrections to basis incompleteness in molecular SCF calculations

A unified summary is presented of the mathematical approach developed by McDowell for employing perturbation theory to correct for basis-set incompleteness in ab initio SCF calculations. Revised expressions for the corrections to the wavefunction both in terms of orbitals and spin-orbitals are presented with explicit incorporation of the spin variables. Employing H₂O as an example, we show that this approach is considerably more powerful for computing molecular energies with standard basis sets than was indicated by previous work. In particular at the higher levels of approximation it accurately reproduces the effect of polarization functions in sets such as 6-31G^* and 6-31G^**. The equilibrium molecular structure of H₂O was also computed by this approach and found to give good accuracy. In each case perturbing functions coupled to both occupied and virtual orbitals are required for acceptable results.     

Determination and characterization of a transition structure for water–formaldehyde addition

Quantum mechanical calculations of the geometric, energetic, electronic, and vibrational features of a transition structure for gas-phase water–formaldehyde addition (FW1?) are described, and a new transition-structure search algorithm is presented. Basis-set-dependent effects are assessed by comparisons of computed properties obtained from self-consistent field (SCF) molecular orbital (MO) calculations with STO-3G, 4-31G, and 6-31G^** basis sets in the absence of electron correlation. The results obtained suggest that STO-3G-level calculations may be sufficiently reliable for the prediction of the transition structure of FW1? and for the transition structures of related carbonyl addition reactions. Moreover, the calculated activation energy for formation of FW1? from water and formaldehyde (?44 kcal mol^?1) is very similar in all three basis sets. However, the energy of formaldehyde hydration predicted by STO-3G (? ?45 kcal mol^?1) is about three times larger than that predicted by the other two basis sets, with the activation energy for dihydroxymethane dehydration also being too large in STO-3G. Calculated force constants in all three basis sets are generally too large, leading to vibrational frequencies that are also too large. However, uniformly scaled force constants (in internal coordinates) give much better agreement with experimental frequencies, scaled 4-31G force constants being slightly superior to scaled STO-3G force constants.     

Highly efficient implementation of pseudospectral time‐dependent density‐functional theory for the calculation of excitation energies of large molecules

We have developed and implemented pseudospectral time‐dependent density‐functional theory (TDDFT) in the quantum mechanics package Jaguar to calculate restricted singlet and restricted triplet, as well as unrestricted excitation energies with either full linear response (FLR) or the Tamm–Dancoff approximation (TDA) with the pseudospectral length scales, pseudospectral atomic corrections, and pseudospectral multigrid strategy included in the implementations to improve the chemical accuracy and to speed the pseudospectral calculations. The calculations based on pseudospectral time‐dependent density‐functional theory with full linear response (PS‐FLR‐TDDFT) and within the Tamm–Dancoff approximation (PS‐TDA‐TDDFT) for G2 set molecules using B3LYP/6‐31G*^* show mean and maximum absolute deviations of 0.0015 eV and 0.0081 eV, 0.0007 eV and 0.0064 eV, 0.0004 eV and 0.0022 eV for restricted singlet excitation energies, restricted triplet excitation energies, and unrestricted excitation energies, respectively; compared with the results calculated from the conventional spectral method. The application of PS‐FLR‐TDDFT to OLED molecules and organic dyes, as well as the comparisons for results calculated from PS‐FLR‐TDDFT and best estimations demonstrate that the accuracy of both PS‐FLR‐TDDFT and PS‐TDA‐TDDFT. Calculations for a set of medium‐sized molecules, including C_n fullerenes and nanotubes, using the B3LYP functional and 6‐31G^** basis set show PS‐TDA‐TDDFT provides 19‐ to 34‐fold speedups for C_n fullerenes with 450–1470 basis functions, 11‐ to 32‐fold speedups for nanotubes with 660–3180 basis functions, and 9‐ to 16‐fold speedups for organic molecules with 540–1340 basis functions compared to fully analytic calculations without sacrificing chemical accuracy. The calculations on a set of larger molecules, including the antibiotic drug Ramoplanin, the 46‐residue crambin protein, fullerenes up to C₅₄₀ and nanotubes up to 14×(6,6), using the B3LYP functional and 6‐31G^** basis set with up to 8100 basis functions show that PS‐FLR‐TDDFT CPU time scales as N^2.05 with the number of basis functions. © 2016 Wiley Periodicals, Inc.     

Eclipsed and staggered conformations of (SIH3)2F+: An ab initio study

Ab initio calculations at 6–31G**, 6–31++G**, and MP2/6–31G** levels were performed on disilyl–fluoronium, (SiH₃)₂F⁺, with the SiH₃ group eclipsed or staggered. Optimized geometries, total energies, dipole moments, atomic charges, electronic density, and vibrational frequencies were computed. The results were compared with calculated structural parameters and vibrational frequencies of H₃SiF, H₂SiF⁺, H₂SiF^?, and H₄SiF⁺ ions. The basis-set effects were studied. Several thermochemistry parameters—ZPE, thermal energy, rotational constants, and entropies—were also calculated. © 1994 John Wiley & Sons, Inc.     

The effect of including polarization functions on the geometrical parameters calculated for pyridine

Geometrical parameters for pyridine have been calculated using the 6-31G, 6-31G^*(5D), 6-31G^**(6D), and 6-31G(2 × 6D) basis sets. Comparisons are made with a microwave substitution structure and with results of other ab initio calculations reported in the literature. Particular attention is paid to the influence of polarization functions on the magnitude of the ring angle, 〈C₆N₁C₂, which is analogous to the ipso angle in monosubstituted benzene derivatives.     

Ab initio and molecular mechanics study of n-phenyl phthalimide and its crystal structure

Ab initio molecular orbital calculations are reported on the energetics for torsional motion of N-phenyl phthalimide using 3-21G, 6-31G, and 6-31G^** basis sets and incorporating electron correlation effects for selected geometries. With the largest basis set, a minimum energy is found for a torsion angle of 59.2°. Atomic charges are assigned to the molecules on the basis of a least-squares fit to the molecular electrostatic potential. This information is then used in molecular mechanics calculations of the crystal structure, where the calculated unit cell parameters are in good agreement with those observed experimentally.     

Rotational barriers of disilane,hexafluorodisilane, and hexamethyldisilane: Ab initio,density functional,and molecular mechanics (MM3) studies

We investigated structures, vibrational frequencies, and rotational barriers of disilane (Si₂H₆), hexafluorodisilane (Si₂F₆), and hexamethyldisilane (Si₂Me₆) by using ab initio molecular orbital and density functional theories. We employed four different levels of theories (i.e., HF/6–31G*, MP2/6–31G*, BLYP/6–31G*, and B3LYP/6–31G*) to optimize the structures and to calculate the vibrational frequencies (except for Si₂Me₆ at MP2/6–31G*). MP2/6–31G* calculations reproduce experimental bond lengths well, while BLYP/6–31G* calculations largely overestimate some bond lengths. Vibrational frequencies from density functional theories (BLYP/6–31G* and B3LYP/6–31G*) were in reasonably good agreement with experimental values without employing additional correction factors. We calculated the ΔG^‡(298 K) values of the internal rotation by correcting zero-point vibration energies, thermal vibration energies, and entropies. We performed CISD/6–31G*//MP2/6–31G* calculations and found the ΔG^‡(298 K) values for the internal rotation of Si₂H₆, Si₂F₆, and Si₂Me₆ to be 1.36, 2.06, and 2.69 kcal/mol, respectively. The performance of this level was verified by using G2 and G2(MP2) methods in Si₂H₆. According to our theoretical results, the ΔG^‡(298 K) values were marginally greater than the ΔE^‡(0 K) values in Si₂F₆ and Si₂Me₆ due to the contribution of the entropy. In Si₂H₆ the ΔE^‡(0 K) and ΔG^‡(298 K) values were coincidently similar due to a cancellation of two opposing contributions between zero-point and thermal vibrational energies, and entropies. Our calculated ΔG^‡(298 K) values were in good agreement with experimental values published recently. In addition, we also performed MM3 calculations on Si₂H₆ and Si₂Me₆. MM3 calculated rotational barriers and thermodynamic properties were compared with high level ab initio results. Based on this comparison, MM3 calculations reproduced high level ab initio results in rotational barriers and thermodynamic properties of Si₂H₆ derivatives including vibrational energies and entropies, although large errors exist in some vibrational frequencies. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1523–1533, 1997     

The 6-31G++ basis set: An economical basis set for correlated wavefunctions

The 6-31G ⁺⁺ basis set is described. This basis set is very similar to the existing 6-31G ^** set but is somewhat smaller through the use of five (rather than six) second-order Gaussians (d functions) and has polarization function exponents optimized for correlated rather than Hartree–Fock wavefunctions. The performance of 6-31G ⁺⁺ is compared with that of the 6-31G ^** and 6-31G ^** basis sets through calculation of the geometries and atomization energies for the set of molecules LiH, FH, H₂O, NH₃, CH₄, N₂, CO, HCN, and HCCH.     

Ab initio studies of F−(H2O)n and Cl−(H2O)n clusters for n = 1, 2

Ab initio Hartree–Fock calculations are performed on hydrates of the F^? and Cl^? ions using 6-31G, 6-31G**, and 6-21G basis sets. Geometries and binding energies are obtained. An estimate of the correlation energy is provided by an MP2/6-31G (Møller-Plesset second-order perturbation) calculation. Comparisons are made between the Cl^?(SO₂) and the Cl^?(H₂O) complexes.     

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.     

On the additivity of basis set effects in some simple fluorine containing systems

The reactions F + H₂ → HF + H, HF → H + F, F → F⁺ + e^? and F + e^? → F^? were used as simple test cases to assess the additivity of basis set effects on reaction energetics computed at the MP4 level. The 6-31G and 6-311G basis sets were augmented with 1, 2, and 3 sets of polarization functions, higher angular momentum polarization functions, and diffuse functions (27 basis sets from 6-31Gd, p) to 6-31 ++ G(3df, 3pd) and likewise for the 6-311G series). For both series substantial nonadditivity was found between diffuse functions on the heavy atom and multiple polarization functions (e.g., 6-31 + G(3d, 3p) vs. 6-31 + G(d, p) and 6-31G(3d, 3p)). For the 6-311G series there is an extra nonadditivity between d functions on hydrogen and multiple polarization functions. Provided that these interactions are taken into account, the remaining basis set effects are additive to within ±0.5 kcal/mol for the reactions considered. Large basis set MP4 calculations can also be estimated to within ±0.5 kcal/mol using MP2 calculations, est. E_MP4(6-31 ++ G(3df, 3pd)) ≈ E_MP4(6-31G(d, p)) + E_MP2(6-31 ++ G(3df, 3pd)) – E_MP2(6-31G(d, p)) or E_MP4(6-31 + G(d, p) + E_MP2(6-31 ++ G(3df, 3pd)) – E_MP2(6-31 + G(d, p)) and likewise for the 6-311G series.     

Intramolecular Hypervalent X←X Interaction in Mono- and Bicyclic Heteroelement Compounds Containing Se and Te Atoms

Chalcogen-containing heterapentalene and quasimonocyclic compounds having SeÄSeÄSe and TeÄTeÄTe triads or SeÄSe and TeÄTe diads were studied by the ab initio [MP2(full)/6-31G**, MP2(fc)/6-31+G**, and MP2(fc)/LANL2DZ] and DFT methods (B3LYP/6-31G^**, B3LYP/6-31+G^**, and B3LYP/LANL2DZ). Heterapentalene compounds were found to be stable as planar bicyclic structures having a C _2v symmetry. The stability of quasimonocycic -chalcogenovinyl aldehydes increases with increase in the electron-acceptor power of the substituent at the X atom.     

Infrared experimental and ab initio quantum mechanical studies of 2-mercaptopyrimidine tautomers

Results are presented from ab initio SCF(3-21G*) calculations for the geometries and vibrational spectra (wavenumbers and absolute intensifies) of the thiol and thione tautomers of 2-mercaptopyrimidine. The results of calculations are compared with available experimental data, particularly with the reported vibrational spectra of the molecule isolated in inert gas matrices (Ar, N₂) and in crystalline state. The calculations of the normal modes predicted the experimental spectrum close enough to allow reliable assignment of most of the bands. The thiol⇌⇌thione tautomerism of the molecule is discussed. Matrix isolated monomers were observed in the thiol form only. That agrees with the results of ab initio calculations of internal energies of the tautomers [SCF(6-31Gu*) + MBPT(2)(6-31G*) + vib(0)(3-21G*); at the SCF(3-21G*) geometries] which predict the energy of thiol form to be ≈33 kJ mol⁻¹ lower than that of thione form. In the crystalline state the hydrogen-bonded associations in the thione form dominate while in disordered amorphous layers, in matrices with a high guest-to-host ratio and in annealed matrices the associations both in thiol and thione form were observed.     

The C−NO2 bond dissociation energies of some nitroaromatic compounds: DFT study

The C−NO₂ bond dissociation energies in nitrobenzene; 3-amino-nitrobenze; 4-amino-nitrobenze; 1,3-dinitrobenzene; 1,4-dinitrobenzene; 2-methyl-nitrobenzene; 4-methyl-nitrobenzene; and 1,3,5-trinitrobenzene nitroaromatic molecules, are computed using B3LYP, B3PW91, B3P86 three-parameter hybrid Density Functional Theory (DFT) methods in conjunction with 6-31G^** basis set. By comparing the computed energies and experimental ones, it is found that B3P86/6-31G^** is not capable of predicting the satisfactory bond dissociation energy (BDE). The BDEs computed with both B3LYP/6-31G^** and B3PW91/6-31G^** for the nitroaromatic molecules are closer to the experimental ones than those obtained with B3P86/6-31G^**. But, when compared with the experimental one, the BDE from the B3LYP/6-31G^** has the maximum deviation, which is completely outside our desired target accuracy for chemical predictions (less than 2.00 kcal mol⁻¹). Therefore, we suggest B3PW91/6-31G^** method as a reliable method of computing the BDE for removal of the nitrogen dioxide group in the nitroaromatic compounds. In addition, the C−NO₂ BDEs for 2,4,6-trinitrotoluene (TNT), triaminotrinitrobenzene (TATB), diaminotrinitrobenzene (DATB), and picramide are studied with B3PW91/6-31G^** method.     

Proton and sodium ion affinities of glycine and its sodium salt in the gas phase. Ab initio calculations

The energies of protonation and Na⁺ cationization of glycine (GLY) and its (GLY ? H + Na) salt in the gas phase were calculated using ab inltio calculations. The proton affinity of GLY, valued at the MP2/6–31G*//3-21G level, is 937 kJ mol^?1. The amino function is confirmed to be the most favourable site of protonation: ‘proton affinities’ of the carbonyl and hydroxyl functions are calculated to be 75 and 180 kJ mol^?1, respectively, lower than that of NH₂ at the MP2/6-31G*//3–21G level. Calculations performed up to the MP2/6–31G*//3–21G level give the Na⁺ affinity of GLY as 189 kJ mol^?1 and the H⁺ and Na⁺ affinities of (GLY – H + Na) as 1079 and 298 kJ mol^?1, respectively. The geometries of all neutral and protonated species optimized with the 3–21G basis set are described. Both H* and Na⁺ cations complex preferably between the nitrogen atom and the carbonyl oxygen atom, leading to pseudo-five-membered ring structures in which Na? O and Na? N bonds lengths are greater than 2 Å.     

AB initio calculations of 2H and 14N quadrupolar coupling constants in hydrogen bonded dimers

SCF MO calculations at the 6-31G^** level of approximation are reported for ²H and ¹⁴N electric field gradients in HCN?HCN, HCN?HF, and CH₃CN?HF dimers, with emphasis on the configurational dependence of these quantities in (HCN)₂. In comparison with available experimental nuclear quadrupolar coupling constants, the calculated values for the monomers and dimers exhibit an accuracy of ≈ 10%, which is comparable to that of other spectroscopic parameters. The implications of hydrogen bonding for quadrupolar spin-lattice relaxation rates are briefly discussed.     

Potential energy surfaces for the molecular and free radical dissociations of H2CS,F2CS and Cl2CS: An ab initio SCF MO study

Energies along the planar symmetric (C_2v) and planar assymetric (C_s paths to molecular dissociation of the ground state thiocarbonyl halides, F₂CS and Cl₂CS, together with their transition state geometries, have been calculated by ab initio SCF MO methods using the STO-3G and 4-31G basis sets. For comparison, results on H₂CS at similar levels of calculation are also included in this report. In addition, the 4-31G^** basis set has been employed to predict the geometries of the ground state species and the endothermicities of their free radical dissociations. The results of experiments in which the lowest excited singlet states of these molecules have been photoexcited are interpreted in light of these calculations. Thermodynamic data for both molecular and free radical dissociations are evaluated and discussed.     

Cooperative atomic migrations in the associates of formic acid molecule with H2O...X systems (X=CH3OH,NH2OH,H2O2, HOF,and H2O)

The pathways and activation barriers of cooperative biproton migrations in the associates of the formic acid molecule with H₂O and X molecules (X=CH₃OH, NH₂OH, H₂O₂, FOH, and H₂O) are calculated by an ab initio method (3-21G and 6-31G^** basis sets). A cooperative triproton transfer occurs in the system with X=H₂O. The activation barriers of this transfer calculated in the 3-21G and 6-31G^** basis sets are 6.94 and 27.29 (through the structure of C₂ symmetry) or 7.99 and 26.08 kcal/mole (through the structure of C_s symmetry), respectively. In the systems with X=H₃COH, HOOH, and FOH, the biproton transfer is accompanied by synchronous shifts of two hydroxyl groups and overcomes high activation barriers (>40 kcal/mole), which is accounted for by poor stereochemical similarity for the low-barrier cooperative processes in the given molecular associates. Scientific Research Institute of Physical and Organic Chemistry, Rostov State University. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 5, pp. 845–858, September–October, 1996. Translated by I. Izvekova     

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.