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     

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.     

Compton profiles and polarizability as two similar probes of the electronic structure of 14 electron diatomic molecules: An ab initio study

High‐ and low‐energy scattering properties, namely, Compton profiles and polarizability, respectively, were calculated at the configuration interaction (CI) level from molecular orbitals expressed in the linear combination of atomic orbitals (LCAO) model for 14 electron diatomic molecules. Extended atomic basis sets including about 100 Gaussian‐type functions (GTFs) were used. The isotropic and directional Compton profiles and the polarizability show that the behavior of CO and N₂ is rather similar but very different from that of BF. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 71: 63–74, 1999     

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     

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.     

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.     

A homology/ab initio hybrid algorithm for sampling near‐native protein conformations

One of the major challenges for protein tertiary structure prediction strategies is the quality of conformational sampling algorithms, which can effectively and readily search the protein fold space to generate near‐native conformations. In an effort to advance the field by making the best use of available homology as well as fold recognition approaches along with ab initio folding methods, we have developed Bhageerath‐H Strgen, a homology/ab initio hybrid algorithm for protein conformational sampling. The methodology is tested on the benchmark CASP9 dataset of 116 targets. In 93% of the cases, a structure with TM‐score ≥ 0.5 is generated in the pool of decoys. Further, the performance of Bhageerath‐H Strgen was seen to be efficient in comparison with different decoy generation methods. The algorithm is web enabled as Bhageerath‐H Strgen web tool which is made freely accessible for protein decoy generation ( http://www.scfbio‐iitd.res.in/software/Bhageerath‐HStrgen1.jsp ). © 2013 Wiley Periodicals, Inc.     

Electrophilic attack on sulfur-sulfur bonds: coordination of lithium cations to sulfur-rich molecules studied by ab initio MO methods

Complex formation between gaseous Li+ ions and sulfur-containing neutral ligands, such as H2S, Me2Sn (n = 1-5; Me = CH3) and various isomers of hexasulfur (S6), has been studied by ab initio MO calculations at the G3X(MP2) level of theory. Generally, the formation of LiS(n) heterocycles and clusters is preferred in these reactions. The binding energies of the cation in the 29 complexes investigated range from -88 kJ mol(-1) for [H2SLi]+ to -189 kJ mol(-1) for the most stable isomer of [Me2S5Li]+ which contains three-coordinate Li+. Of the various S6 ligands (chair, boat, prism, branched ring, and triplet chain structures), two isomeric complexes containing the S5==S ligand have the highest binding energies (-163+/-1 kJ mol(-1)). However, the global minimum structure of [LiS6]+ is of C(3v) symmetry with the six-membered S(6) homocycle in the well-known chair conformation and three Li--S bonds with a length of 256 pm (binding energy: -134 kJ mol(-1)). Relatively unstable isomers of S6 are stabilized by complex formation with Li+. The interaction between the cation and the S6 ligands is mainly attributed to ion-dipole attraction with a little charge transfer, except in cations containing the six sulfur atoms in the form of separated neutral S2, S3, or S4 units, as in [Li(S3)2]+ and [Li(S2)(S4)]+. In the two most stable isomers of the [LiS6]+ complexes, the number of S--S bonds is at maximum and the coordination number of Li+ is either 3 or 4. A topological analysis of all investigated complexes revealed that the Li--S bonds of lengths below 280 pm are characterized by a maximum electron-density path and closed-shell interaction.     

CopperII-mediated aromatic ortho-hydroxylation: a hybrid DFT and AB initio exploration

Mechanistic pathways for the aromatic hydroxylation by [CuII(L1)(TMAO)(O)](-) (L1=hippuric acid, TMAO=trimethylamine N-oxide), derived from the O--N bond homolysis of its [CuII(L1)(TMAO)2] precursor, were explored by using hybrid density functional theory (B3LYP) and highly correlated ab initio methods (QCISD and CCSD). Published experimental studies suggest that the catalytic reaction is triggered by a terminal copper-oxo species, and a detailed study of electronic structures, bonding, and energetics of the corresponding electromers is presented. Two pathways, a stepwise and a concerted reaction, were considered for the hydroxylation process. The results reveal a clear preference for the concerted pathway, in which the terminal oxygen atom directly attacks the carbon atom of the benzene ring, leading to the ortho-selectively hydroxylated product. Solvent effects were probed by using the PCM and CPCM solvation models, and the PCM model was found to perform better in the present case. Excellent agreement between the experimental and computational results was found, in particular also for changes in reactivity with derivatives of L1.     

Thioformaldehyde S-methylide and thioacetone S-methylide: an ab initio MO study of structure and cycloaddition reactivity

The mechanisms of cycloaddition of thioformaldehyde S-methylide and thioacetone S-methylide, as models for an alkyl-substituted ylide, to thioformaldehyde and thioacetone, as well as to ethene as a model for a C=C double bond have been studied by ab initio calculations. Restricted and unrestricted B3LYP/6-31G* calculations were performed for the geometries of ground states, transition structures, and intermediates. Although basis sets with more polarization functions were tested, the 6-31G* basis set was applied throughout. Single-point CASPT2 calculations are reported for analysis of the unsubstituted system. The stabilities of structures with high biradical character seem to be overestimated by DFT methods in comparison to CASPT2. The general trends of the results are independent of the level of theory. Thioformaldehyde adds to thioformaldehyde S-methylide without activation energy, and the activation energies for two-step biradical pathways to 1,3-dithiolane are low. C,S biradicals are more stable than C,C biradicals. The two-step cycloaddition is not competitive with the concerted cycloaddition. Methyl substitution in the 1,3-dipole and the dipolarophile does not change the mechanistic relationships. TSs for the concerted formation of the regioisomeric cycloadducts of thioacetone Smethylide and thioacetone were located. Concerted addition remains the preferred reaction. The reactivity of the C=S double bond is high relative to that of the C=C double bond.     

Photochemical and electronic properties of conjugated bis(azo) compounds: an experimental and computational study

We have investigated the photophysical, photochemical and electrochemical properties of two bis(azo) derivatives, (E,E)-m-1 and (E,E)-p-1. The two compounds, which can be viewed as being composed of a pair of azobenzene units sharing one of their phenyl rings, differ only for the relative position of the two azo groups on the central phenyl ring-meta and para for m-1 and p-1, respectively. The UV-visible absorption spectra and photoisomerisation properties are noticeably different for the two structural isomers; (E,E)-m-1 behaves similarly to (E)-azobenzene, while (E,E)-p-1 exhibits a substantial red shift in the absorption bands and a decreased photoreactivity. The three geometric isomers of m-1, namely the E,E, E,Z and Z,Z isomers, cannot be resolved in a mixture by absorption spectroscopy, while the presence of three distinct species can be revealed by analysis of the absorption changes observed upon photoisomerisation of (E,E)-p-1. Quantum chemical ZINDO/1 calculations of vertical excitation energies nicely reproduce the observed absorption changes and support the idea that, while the absorption spectra of the geometrical isomers of m-1 are approximately given by the sum of the spectra of the constituting azobenzene units in their relevant isomeric form, this is not the case for p-1. From a detailed study on the E-->Z photoisomerisation reaction it was observed that the photoreactivity of an azo unit in m-1 is influenced by the isomeric state of the other one. Such observations indicate a different degree of electronic coupling and communication between the two azo units in m-1 and p-1, as confirmed by electrochemical experiments and quantum chemical calculations. The decreased photoisomerisation efficiency of (E,E)-p-1 compared to (E,E)-m-1 is rationalised by modelling the geometry relaxation of the lowest pi-pi* state. These results are expected to be important for the design of novel oligomers and polymers, based on the azobenzene unit, with predetermined photoreactivity.     

Noncovalent complexes between dimethyl ether and formic acid--an ab initio and matrix isolation study.

The complexes formed by noncovalent interactions between formic acid and dimethyl ether are investigated by ab initio methods and characterized by matrix isolation spectroscopy. Six complexes with binding energies between -2.26 and -7.97 kcal mol(-1) (MP2/cc-pVTZ+zero point vibrational energy+basis set superposition erros) are identified. The two strongest bound complexes are, within a range of 0.3 kcal mol(-1), isoenergetic. The binding in these six dimers can be described in terms of OH...O, C=O...H, C-O...H and CH...O interactions. Matrix isolation spectroscopy allowed to characterize the two strongest bound complexes by their infrared spectra.     

Single‐ and double‐electron reductions of CO2 by using superalkalis: An ab initio study

CO₂, a major contributor to global warming, can be balanced by converting it into fuels. The reduction of CO₂ has been difficult due to its extremely high stability. Recently, single‐electron reduction of CO₂ by superalkalis has been proposed using quantum chemical methods. Herein, we report a systematic study on the single‐reduction of CO₂ by using typical superalkalis. Superalkalis are hypervalent species possessing lower ionization energies than alkali atoms. We have studied the interaction of CO₂ with FLi₂, OLi₃, and NLi₄ superalkalis using ab initio MP2 calculations. We notice that this interaction leads to stable superalkali‐CO₂ complexes in which the structure of CO₂ is bent due to electron transfer from superalkalis. This clearly reveals that the CO₂ can successfully be reduced to the anion. It has been also noticed that the size of superalkalis plays a crucial in the single‐electron reduction of CO₂. For instance, the binding energy of superalkali‐CO₂ complex and charge transfer to CO₂ decreases monotonically with the increase in the size of superalkali. We have also proposed that CO₂ can be further reduced to in case of the anionic complex such as (FLi₂ CO₂)‾. Thus, FLi₂ superalkali is also capable of double‐electron reduction of CO₂. These findings should provide new insights into CO₂‐activation as well as motivate further research in this direction.     

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.     

High‐level ab initio computational study of doublet and quartet nitrogen reaction with methane

High levels of ab initio calculations were performed with the target of exploring the potential‐energy surface for the doublet and the quartet nitrogen with methane. There is a considerable difference between these two reaction paths in light of the formation of the reactant complex. Doublet nitrogen is an excited state of nitrogen, but it forms a stronger complex with methane, making the activation barrier with the doublet and quartet nitrogen reaction with methane. Activation barriers, heats of the reaction, and bond dissociation energies for minima located in the potential surface of nitrogen and methane transformations into the hydrogen radical and H₂CNH were evaluated, and the most probable reaction pathways were suggested. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 71: 481–490, 1999     

FA(I):A(+) and FA(II):Cu(+) laser activity and photographic sensitization at the low coordinated surfaces of AgBr ab initio calculations

The twofold potentials of F(A)(I):Au(+) and F(A)(II)Cu(+) color centers at the low coordinated surfaces of AgBr thin films in providing tunable laser activity and photographic sensitization were investigated using ab initio methods of molecular electronic structure calculations. Clusters of variable size were embedded in simulated Coulomb fields that closely approximated the Madelung fields of the host surfaces, and the nearest neighbor ions to the F(A) defect site were allowed to relax to equilibrium in each case. Based on the calculated Stokes shifted optical transition bands and horizontal shifts along the configuration coordinate diagrams, both F(A)(I):Au(+) and F(A)(II):Cu(+) color centers were found to be laser active. The laser activity faded quickly as the bromide ion coordination decreased from 5 (flat) to 4 (edge) to 3 (corner) and as the size of the impurity cation increased from Cu(+) to Au(+). The latter relation was explainable in terms of the axial perturbation of the impurity cation. The smallest calculated Stokes-shift at the corner surface suggested that emission had the same oscillator strength as absorption. All relaxed excited states RESs of the defect containing surfaces were deep below the lower edges of the conduction bands of the defect free ground state surfaces, indicating that F(A)(I):Au(+) and F(A)(II):Cu(+) are suitable laser defects. The probability of orientational destruction of the two centers attributed to the assumed RES saddle point ion configurations along the <110> axis was found to be directly proportional to the size of the impurity cation, with activation energy barriers of about 0.655-3.294 eV for Cu(+), and about 1.887-3.404 eV for Au(+). The possibility of exciton (energy) transfer from the sites of higher coordination to those of lower coordination is demonstrated. The more laser active F(A)(II):Cu(+) center was more easily formed than the less laser active F(A)(I):Au(+) center. The Glasner-Tompkins empirical relation was generalized to include F(A) centers at the low coordinated surfaces of silver bromide thin film. As far as color photographic sensitization is concerned, the lowest unoccupied molecular orbitals of the selected dye molecules in the excited states were high enough for electron injection. F(A) defect formation and rotational diffusion of silver clusters reduced the energy gaps between the excited dye molecules and the lower edges of the conduction bands and allowed for hole injection. About 54-60% of the reduction of silver ions at the flat surface of AgBr was attributed to the host anions and F(A) defect formation, leaving about 40-46% for the reduction of photoelectrons as well as the electrons of the developer or dye molecules. The unrelaxed rotational diffusions of the central Ag(4) by 90 degrees decreased the latter percentage, but were severely hindered by activation energy barriers.     

Photophysics of eumelanin: ab initio studies on the electronic spectroscopy and photochemistry of 5,6-dihydroxyindole.

Excited-state reaction paths and energy profiles of 5,6-dihydroxyindole (DHI), one of the elementary building blocks of eumelanin, have been determined with the approximated singles-and-doubles coupled-cluster (CC2) method. 6-Hydroxy-4-dihydro-indol-5-one (HHI) is identified as a photochromic species, which is formed via nonadiabatic hydrogen migration from the dangling OH group of DHI to the neighboring carbon atom of the six-membered ring. It is shown that HHI is a typical excited-state hydrogen-transfer (ESIHT) system. HHI absorbs strongly in the visible range of the spectrum. A barrierless hydrogen transfer in the (1)pipi* excited state, followed by barrierless torsion of the hydroxyl group, lead to a low-lying S(1)-S(0) conical intersection and thus to ultrafast internal conversion. This very efficient mechanism of excited-state deactivation provides HHI with a high degree of intrinsic photostability. It is suggested that the metastable photochemical product HHI plays an essential role for the photoprotective biological function of eumelanin.     

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.