DNA base trimers: empirical and quantum chemical ab initio calculations versus experiment in vacuo

A complete scan of the potential‐energy surfaces for selected DNA base trimers has been performed by a molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The resulting most stable/populated structures were then reoptimized at a correlated ab initio level by employing resolution of the identity, Møller–Plesset second‐order perturbation theory (RI‐MP2). A systematic study of these trimers at such a complete level of electronic structure theory is presented for the first time. We show that prior experimental and theoretical interpretations were incorrect in assuming that the most stable structures of the methylated trimers corresponded to planar systems characterized by cyclic intermolecular hydrogen bonding. We found that stacked structures of two bases with the third base in a T‐shape arrangement are the global minima in all of the methylated systems: they are more stable than the cyclic planar structures by about 10 kcal mol^?1. The different behaviors of nonmethylated and methylated trimers is also discussed. The high‐level geometries and interaction energies computed for the trimers serve also as a reference for the testing of recently developed density functional theory (DFT) functionals with respect to their ability to correctly describe the balance between the electrostatic and dispersion contributions that bind these trimers together. The recently reported M052X functional with a polarized triple‐zeta basis set predicts 11 uracil trimer interaction energies with a root‐mean‐square error of 2.3 kcal mol^?1 relative to highly correlated ab initio theoretical calculations.     

The mechanism of formamide hydrolysis in water from ab initio calculations and simulations

The neutral hydrolysis of formamide in water is a suitable reference to quantify the efficiency of proteolytic enzymes. However, experimental data for this reaction has only very recently been obtained and the kinetic constant determined experimentally is significantly higher than that predicted by previous theoretical estimations. In this work, we have investigated in detail the possible mechanisms of this reaction. Several solvent models have been considered that represent a considerable improvement on those used in previous studies. Density functional and ab initio calculations have been carried out on a system which explicitly includes the first solvation shell of the formamide molecule. Its interaction with the bulk has been treated with the aid of a dielectric continuum model. Molecular dynamics simulations at the combined density functional/molecular mechanics level have been carried out in parallel to better understand the structure of the reaction intermediates in aqueous solution. Overall, the most favored mechanism predicted by our study involves two reaction steps. In the first step, the carbonyl group of the formamide molecule is hydrated to form a diol intermediate. The corresponding transition structure involves two water molecules. From this intermediate, a water-assisted proton transfer occurs from one of the hydroxy groups to the amino group. This reaction step may lead either to the formation of a new reaction intermediate with a marked zwitterionic character or to dissociation of the system into ammonia and formic acid. The zwitterionic intermediate dissociates quite easily but its lifetime is not negligible and it could play a role in the hydrolysis of substituted amides or peptides. The predicted pseudo-first-order kinetic constant for the rate-limiting step (the first step) of the hydrolysis reaction at 25 degrees C (3.9x10(-10) s(-1)) is in excellent agreement with experimental data (1.1x10(-10) s(-1)).     

Electron delocalization and electrostatic repulsion at the origin of the strong spin coupling in mixed-valence keggin polyoxometalates: ab initio calculations of the one- and two-electron processes

We present here a general theoretical procedure to treat the problem of electron delocalization and magnetic interactions in high-nuclearity mixed valence clusters based on polyoxometalates. The main interactions between the delocalized electrons of mixed-valence polyoxometalate anions are extracted from valence spectroscopy ab initio calculations on embedded fragments. Electron transfer, magnetic coupling and exchange transfer parameters between nearest and next-nearest-neighbor metal ions, as well as the value of the electrostatic repulsion between pairs of metal ions are determined. These parameters are introduced in a model Hamiltonian that considers the whole anion. It thus provides macroscopic properties that should be compared with the experimental data. This method is applied to a two-electron-reduced polyoxowolframate Keggin anion. The results demonstrate that the electron transfer processes, combined with the Coulombic repulsion between the "extra" electrons, induce a strong antiferromagnetic coupling between the two delocalized spins providing a definite explanation of the diamagnetic properties of these high nuclearity mixed-valence clusters.     

A theoretical ab initio study on the H(2)NO + O(3) reaction

The deviation of the NH(2) pseudo-first-order decay Arrhenius plots of the NH(2) + O(3) reaction at high ozone pressures measured by experimentalists, has been attributed to the regeneration of NH(2) radicals due to the subsequent reactions of the products of this reaction with ozone. Although these products have not yet been characterized experimentally, the radical H(2)NO has been postulated, because it can regenerate NH(2) radicals through the reactions: H(2)NO + O(3) --> NH(2) + O(2) and H(2)NO + O(3) --> HNO + OH + O(2). With the purpose of providing a reasonable explanation from a theoretical point of view to the kinetic observed behaviour of the NH(2) + O(3) system, we have carried ab initio electronic structure calculations on both H(2)NO + O(3) possible reactions. The results obtained in this article, however, predict that of both reactions proposed, only the H(2)NO + O(3) --> NH(2) + O(2) reaction would regenerate indeed NH(2) radicals, explaining thus the deviation of the NH(2) pseudo-first-order decay observed experimentally.     

Spectroscopic properties in the liquid phase: combining high-level ab initio calculations and classical molecular dynamics.

We present an integrated computational tool, rooted in density functional theory, the polarizable continuum model, and classical molecular dynamics employing spherical boundary conditions, to study the spectroscopic observables of molecules in solution. As a test case, a modified OPLS-AA force field has been developed and used to compute the UV and NMR spectra of acetone in aqueous solution. The results show that provided the classical force fields are carefully reparameterized and validated, the proposed approach is robust and effective, and can also be used by nonspecialists to provide a general and powerful complement to experimental techniques.     

Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations

The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum-chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug-cc-pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled-cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density-functional tight-binding methods covering dispersion energy (DFTB-D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein-inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution.     

DFT and ab initio calculations on two reactions between hydrogen atoms and the fire suppressants 2-H heptafluoropropane and CF3Br

Reaction enthalpies and barrier heights of the reactions CF3Br+H-->CF3+HBr {reaction (1)} and CF3CHFCF3+H-->CF3CFCF3+H2 {reaction (2)} have been calculated at the near state-of-the-art ab initio level, and also by employing the B3LYP, BH&HLYP, BB1K, MPW1K, MPWB1K and TPSS1KCIS functionals. In addition, the integrated molecular orbital+molecular orbital (IMOMO) method has been used to study reaction (2). The ab initio benchmark values of the reaction enthalpy (298 K) and barrier height (0 K) of reaction (2) are reported for the first time {-(0.7+/-0.7) and 13.3+/-0.5 kcal/mole respectively}. When density functional theory (DFT) results are compared with ab initio benchmarks for both reactions (1) and (2), the MPWB1K functional is found to have the best performance of the six functionals used. The IMOMO method with the RCCSD/aug-cc-pVTZ and/or RCCSD(T)/aug-cc-pVTZ levels, as the high levels of calculation on the model system, gives reaction enthalpies and barrier heights of reaction (2), which agree with ab initio benchmark values to within 1 kcal/mole. Computed key geometrical parameters and imaginary vibrational frequencies of the transition state structures of reactions (1) and (2) obtained at different levels of calculation are compared. The magnitudes of the computed imaginary vibrational frequencies of the transition states of both reactions considered are found to be very sensitive to the levels of calculation used to obtain them. The heat of formation (298 K) of CF3CFCF3 calculated at the near state-of-the-art level has a value of -(318+/-3) kcal/mole.     

Rationalization of the behavior of M2(CH3CS2)4I (M = Ni,Pt) chains at room temperature from periodic density functional theory and ab initio cluster calculations

The electrical conductivities and plausible charge‐ordering states in the room temperature (r.t.) phase for MMX chains [Ni₂(dta)₄I]_∞ and [Pt₂(dta)₄I]_∞ (dta = CH₃CS) have been analyzed with periodic density functional theory (DFT) and correlated ab initio calculations combined with the effective Hamiltonian theory. Periodic DFT calculations show a more delocalized nature of the ground state in [Pt₂(dta)₄I]_∞ compared to [Ni₂(dta)₄I]_∞, which features a rather large energy gap between the occupied and empty bands, and charge polarized dimer units. A larger electrical conductivity for the Pt chain can be expected, especially because the Fermi level lies within a band with contributions from Pt and I orbitals. Electronic structure parameters extracted from ab initio cluster calculations show that the large difference between the observed conductivities at 300 K for Ni and Pt compounds, of 3 orders of magnitude, cannot be explained from the parameters extracted from an embedded M₂(dta)₄I₂ dimer fragment alone. When tetramer fragments are considered, we observe that the interdimer transfer integral (t) between neighboring M₂ units connected by an iodine atom at correlated level is comparable in both chains. On the other hand, the energy to transfer an electron from a dimer to the neighboring one (Coulomb repulsion U) is three times larger in the Ni compound with respect to the Pt chain, in line with the poor conductivity of the former. The electronic structure of the M₄(dta)₈I₃ fragment points to an alternate charge‐polarization state for Ni and an average valence state for Pt when the r.t. X‐ray structure is considered. © 2012 Wiley Periodicals, Inc.     

Unimolecular isomerization/decomposition of cyclopentadienyl and related bimolecular reverse process: ab initio MO/statistical theory study

The cyclopentadienyl radical decomposition has been studied in detail by high‐level correlation MO methods combined with multichannel RRKM rate constant calculations. The product channels of the reaction were examined by calculating their pressure‐dependent branching rate constants. The overall reaction rate has been shown to be controlled by the first transition state corresponding to 1,2‐hydrogen atom migration. Also, the reverse bimolecular reactions (C₃H₃ + C₂H₂ → products) have been included in the study. We provide a summary of pressure dependent rate constant expressions for the 1000–3000 K temperature range that may be useful for kinetic modeling of relevant combustion systems. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 415–425, 2000     

Molecular structure of aniline in the gaseous phase: A concerted study by electron diffraction and ab initio molecular orbital calculations

The molecular structure of free aniline has been investigated by gas-phase electron diffraction and ab initio MO calculations at the HF and MP2 levels of theory, using the 6-31G^*(6D) basis set. Least-squares refinement of a model withC _s symmetry, with constraints from MP2 calculations, has led to an accurate determination of the C-C-C angle at theipso position of the benzene ring, =119.0±0.2 (where the uncertainty represents total error). This parameter provides information on the extent of the interaction between the nitrogen lone pair and the system of the benzene ring, and could not be determined accurately by microwave spectroscopy. The angles at theortho, meta, andpara positions of the ring are 120.3±0.1, 120.7±0.1, and 119.0±0.3, respectively. Important bond distances are r _g(C-C)=1.398±0.003 å andr _g(C-N) =1.407±0.003 å. The effective dihedral angle between the H-N-H plane and the ring plane, averaged over the large-amplitude inversion motion of the amino group, is ¦¦=44±4. The equilibrium dihedral angle is calculated to be 41.8 at the HF level and 43.6 at the MP2 level, in agreement with far-infrared spectroscopic information. The MO calculations predict that the differencer(C_ortho-C_meta) -r(C_ipso-C_ortho) is 0.008–0.009 å. They also indicate that the nitrogen atom is displaced from the ring plane, on the side opposite to the amino hydrogens. The displacement is 0.049 å at the HF level and 0.072 å at the MP2 level. The two calculations, however, yield very different patterns for the minute deviations from planarity of the ring carbons.     

A hybrid ab initio/free electron computational model for conjugated dye molecules: Simple cyanines and oxonols

Justifications developed for the application the free electron model to the π‐orbitals of conjugated molecules suggest that the optical properties of these molecules would be well described by a one‐dimensional free electron model with a potential chosen to reproduce the energy level spacing of the ground state occupied π‐orbitals. Such a hybrid ab initio/free electron modeling approach, where the free electron potential parameters are optimized on a molecule‐by‐molecule basis, is developed, and applied to a series of simple cyanine and oxonol dyes. The ensuing predictions for λ_max, oscillator strengths, and redox properties compare well to available experimental information. Two important strengths of this approach are that no explicit calculations of the excited electronic state are required, and that the ab initio determination of the occupied π‐orbital level spacing considers all the electrons (π and σ) of the entire molecule in a specified geometry, environment, etc. This second characteristic gives the ability to efficiently model modifications of the optical properties of conjugated molecules resulting from chemical and/or physical modifications occuring within and remote to the conjugated region of the molecule. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 943–953, 2000     

The singlet-triplet separation in CF2: state-of-the-art ab initio calculations and Franck-Condon simulations including anharmonicity.

Geometrical parameters, vibrational frequencies and relative electronic energies of the X2B1 state of CF2- and the X1A1 and ?3B1 states of CF2 have been calculated. Core-electron effects on the computed minimum-energy geometries and relative electronic energies have been investigated, and relativistic contributions to the computed relative electronic energies calculated. Potential energy functions of the X2B1 state of CF2- and the X1A1 and ?3B1 states of CF2 have been determined, and anharmonic vibrational wavefunctions of these states calculated variationally. Franck-Condon factors including anharmonicity and Duschinsky rotation have been computed and used to simulate the ?-X emission spectrum of CF2 determined by S. Koda [Chem. Phys. Lett. 1978, 55, 353] and the 364 nm laser photodetachment spectrum of CF2- obtained by R. L. Schwartz et al. [J. Phys. Chem. A 1999, 103, 8213]. Comparison between theory and experiment shows that the theoretical approach benchmarked in the present study is able to give highly reliable positions for the CF2(X1A1) + e <-- CF2-(X2B1) and CF2(?3B1) + e <-- CF2-(X2B1) bands in the photoelectron spectrum of CF2- and a reliable singlet-triplet gap for CF2. It is therefore concluded that the same theoretical approach should give reliable simulated CCl2(X1A1) + e <-- CCl2-(X2B1) and CCl2(?3B1) + e <-- CCl2-(X2B1) bands in the photodetachment spectrum of CCl2- and a reliable singlet-triplet gap for CCl2.     

The vibrational and NMR spectra,conformations and ab initio calculations of aminomethylene,propanedinitrile and itsN-methyl derivatives

The IR and Raman spectra of aminomethylene propanedinitrile (AM) [H₂N-CH=C(CN)₂], (methylamino)methylene propanedinitrile (MAM) [CH₃NH-CH=C(CN)₂] and (dimethylamino)methylene propanedinitrile (DMAM) [(CH₃)₂N-CH=C(CN)₂] as solids and solutes in various solvents have been recorded in the region 4000-50 cm^–1. AM and DMAM can exist only as one conformer. From the vibrational and NMR spectra of MAM in solutions, the existence of two conformers with the methyl group orientedanti andsyn toward the double C=C bond were confirmed. The enthalpy difference H ⁰ between the conformers was measured to be 3.7±1.4 kJ mol^–1 from the IR spectra in acetonitrile solution and 3.4±1.1 kJ mol^–1 from the NMR spectra in DMSO solution. Semiempirical (AM1, PM3, MNDO, MINDO3) and ab initio SCF calculations using a DZP basis set were carried out for all three compounds. The calculations support the existence of two conformersanti andsyn for MAM, withanti being 7.8 kJ mol^–1 more stable thansyn from ab initio and 8.6, 13.4, 11.6, and 10.8 kJ mor^–1 from AM1, PM3, MNDO, and MINDO3 calculations, respectively. Finally, complete assignments of the vibrational spectra for all three compounds were made with the aid of normal coordinate calculations employing scaled ab initio force constants. The same scale factors were optimized on the experimental frequencies of all three compounds, and a very good agreement between calculated and experimental frequencies was achieved.     

Adsorption of polyacrylic acid on aluminium oxide: DRIFT spectroscopy and ab initio calculations

Diffuse reflectance Fourier transform infrared (DRIFT) spectroscopy was used to study the adsorption process of the water-soluble polyacrylic acid (PAA) polymer on hydrous δ-Al₂O₃. Vibrational assignment of PAA, sodium polyacrylate, (Na–PA) and the PA-oxide surface complex was achieved by comparison of observed band position and intensity in the DRIFT spectra with wavenumbers and intensities from ab initio quantum mechanical calculations. The presented data of polyacrylic acid suggest that IR data calculated ab initio on relatively short oligomers (quantum-mechanical oligomer approach) may provide valuable information regarding the interpretation of polyelectrolyte infrared spectra. Batch adsorption experiments were performed to sorb PAA onto the δ-Al₂O₃ surface. The results obtained from DRIFT studies were compared with adsorption isotherm experiments in order to relate the level of PAA coverage to the nature of the surface complex. Ab initio molecular orbital calculations on PAA/Al₂O₃ clusters were used to model possible surface complexes. Strong correlation were found between theoretical and observed DRIFT frequencies of the antisymmetric R-COO⁻ vibration. A number of possible configurations of the polyacrylic acid/aluminate surface complex were tested via ab initio calculations. These possible configurations included different di-aluminium octahedral Al³⁺ surface models. Results obtained from adsorption isotherm experiments, DRIFT spectra and ab initio calculations indicate that the carboxylate oxygens bridge an Al³⁺-octahedral dimer [Al₂(OH)₂4(H₂O)2(OH)] in a ligand-exchange inner sphere complex.     

Electronic properties of the low‐lying spin states of dimethylnitrosamine coordinated to Fe(III) heme models: An ab initio study

The unusual O‐coordination mode of nitrosamines to Fe(III) heme models has been observed in the bis(dimethylnitrosamine)(meso‐tetraphenylporphyrinate)iron(III) cation. For the first time, this latter as well as the simpler bis(dimethylnitrosamine)(porphinate)iron(III) heme model cations have been studied through ab initio methods. The sextet, quartet, and doublet spin states of both cations have been studied through single‐point calculations based on the experimental (X‐ray) geometry. Their energies, charges, and spin densities have been analyzed. The obtained results (at the UHF/cc‐pVDZ and ROHF/cc‐pVDZ levels) indicate that the peripheral benzene rings are of secondary importance for the coordination of dimethylnitrosamine to the Fe(III) porphyrin core. The obtained energy ordering is sextet < quartet < doublet, at all computational levels. The UHF, ROHF, and UMP2 results indicate an excess of alpha spin density around the Fe atom, a low covalency for the Fe? O bond and a substantial charge transfer to the Fe atom. Our best estimates [obtained at ROMP2 level with the mixed cc‐pVDZ/cc‐pVTZ‐DK(Fe) basis set] for the energy differences (in eV) between the three spin states considered are 0.929 for the sextet‐quartet gap and 0.812 for the quartet‐doublet gap, which indicate that the spin crossover (at room temperature) is very unlikely. These results represent the substantial decrease in the uncorrelated values. The implications of spin contaminations at the UHF and UMP2 levels for subsequent geometry optimizations to be performed in the smaller cation have also been discussed. © 2013 Wiley Periodicals, Inc.     

Electronic and magnetic structures and conductivity of strontium ferrite: An ab initio LSDA + U approach

Using the first-principle nonempirical linear muffin-tin orbital method in the tight-binding approximation (TB-LMTO) to the LSDA + U approximation, the electronic and magnetic structures and defect formation in strontium ferrite Sr₃Fe₂O₆ are studied. It is found that Sr₃Fe₂O₆ is a G type antiferromagnetic with the semiconductor electronic structure. The calculated band gap of 1.82 eV agrees well with experimental value (～2 eV). The ferrite spectrum corresponds to that of a semiconductor with a band gap of charge transfer. Iron ions in Sr₃Fe₂O₆ are in a high-spin state and have configuration t _2g ^↑3 e _g ^↑2 e _g ^↓1 . The calculated local magnetic moment on the iron ions is 3.9 μ_B. The presence of iron ions with a magnetic moment approaching 4 μ_B in Sr₃Fe₂O₆ is explained by strong hybridization of 3d orbitals of iron and 2p orbitals of oxygen. The high-spin state of iron ions is described by d ⁵ + d ⁶ L states with predominant contribution d ⁶L, where L is a hole on oxygen. Based on ab initio LSDA + U calculations, various types and configurations of defects in the oxygen sublattice (oxygen vacancies, anti-Frenkel defects) are studied and a model for ionic transport in Sr₃Fe₂O₆ is proposed.     

Matrix isolation FT-IR, FT-Raman spectroscopy, conformational ab initio calculations, and vibrational frequencies of meso and racemic-2,4-pentanediol

The infrared spectra of meso-2,4-pentanediol and racemic-2,4-pentanediol were measured in an argon matrix at 20 K. The Raman spectra of the pure liquids (meso and racemic) were measured at room temperature. The spectra were obtained using a Fourier transform spectrophotometer and a cryostat for the low temperature matrix. The meso and racemic forms of the diol were separated by means of a spinning band distillation column. The energies of nine possible conformers of the meso form and nine conformers of the racemic form were calculated. Extensive ab initio calculations using B3LYP, MP2 and HF methods with several basis sets consistently gave the lowest energy for the TT conformer of the meso form and the G⁻T (=TG⁻) conformer of the racemic form. Ab initio calculations at the B3LYP/6-31G** level were performed for the lowest energy conformer of meso and racemic pentanediol to obtain the equilibrium geometry, vibrational frequencies, and infrared and Raman intensities. Calculated and experimental frequencies were compared to make vibrational assignments.     

Complexes of ammonia with propane and cyclopropane: electrostatic guidelines for ab initio treatment

A model based on the molecular electrostatic potential (MESP) is employed for the investigation of structures and energies of complexes of ammonia with propane and cyclopropane. The electrostatic model geometries are employed as starting points for an ab initio investigation at the self-consistent field and second-order M?ller-Plesset (MP2) levels. The most stable structures of C₃H₆..NH₃ and C₃H₈..NH₃ complexes have the interaction energies of 10.07 kJ/mol and 8.15 kJ/mol, respectively, at the MP2/6-31G(d,p) level. The energy rank order of the structures is not altered with the use of the 6-31++G(d,p) basis set, and the basis␣set superposition error has little effect. The interaction energy decomposition analysis shows that the electrostatic component is dominant over the other ones. MESP topography thus seems to offer valuable hints for predicting the structures of weakly bonded complexes. Received: 8 July 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Extrapolation of the linear and nonlinear polarizabilities from ab initio finite oligomer calculations

Different definitions of property per unit cell and different fitting functions are employed to obtain the asymptotic limit values per unit cell of the polarizability (α), the first (β), and the second (γ) hyperpolarizabilities of an infinite oligomer. A 1/n power series function is found to be suitable for the average value and logarithmic average value per unit cell definition, and an exponentially decreasing function is found to be suitable for the difference value per unit cell definition. These conclusions are derived based on an equation expressing the total energy per unit cell of a finite linear oligomer as a power series of 1/n, presented from a perturbation treatment. Several calculations of long chain systems have been carried out to reach our conclusions. An equation of p(n)/n = a + b/n + c/n² is strongly recommended for a least‐squares fitting of the properties per unit cell to achieve a stabilization behavior when the chain length is increased. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006