Predictive abilities of scaled quantum mechanical molecular force fields: application to 2,3-dimethylbuta-1,3-diene

In connection with the appearance of new experimental vibrational data on the high-energy rotational isomer of 2,3-dimethylbuta-1,3-diene (I) in a low-temperature matrix and in neat crystals, the ab initio-based vibrational analysis of this molecule has been re-evaluated. Calculated wavenumbers derived from a scaled quantum-mechanical force field analysis at the MP2(FC)/aug-cc-pVDZ//MP2(FC)/aug-cc-pVDZ computational level are compared with experimental data. Several reassignments of the fundamental wavenumbers for I have been suggested in the course of the current analysis, and the existence of a high-energy non-planar s-gauche conformer of 2,3-dimethylbuta-1,3-diene has been confirmed.     

Infrared spectral identification of the high-energy conformer of <Emphasis Type="Italic">gauche,Trans,trans,Trans,gauche</Emphasis>-octa-1,3,5,7-tetraene

Scaled quantum mechanical force field (SQM-FF) vibrational analyses of the gauche,Trans,trans,Trans,gauche-conformers of octa-1,3,5,7-tetraene (I) with C _i and C ₂ symmetry at the HF/6-31G//HF/6-31G computational level were used to identify the rotational isomer observed in the IR spectrum of this excited molecule in the solid state. Geometry optimizations at the MP2(FC)/aug-cc-pVDZ level show that the two non-planar structures of gTtTg-I have the terminal -CH=CH₂ moieties rotated by ∼30.6° with respect to the remainder of the nearly planar skeleton. The MP2 and HF energies of the C ₂ conformer are slightly lower than the corresponding values of the C _i conformer. A set of the experimental wavenumbers relating to the C ₂ conformer was determined by the detailed analyses of the experimental IR spectra of compounds obtained by Datta et al. via photolysis of 1,3,5-cycloterraene and bicycle[4.2,0]octa-2.4-diene. The available experimental wavenumbers correlate better with the results of our SQM-FF calculations at the HF/6-31G level for the conformer with C ₂ symmetry than for the conformer with C _i symmetry. In further support of these results, the van der Waals molecular volume of the C ₂ conformer was calculated to be somewhat smaller than the volume of the C _i conformer, suggesting that in the solid state, where the close-packing principle comes into play, the C ₂ conformer would be preferred.     

Predictive Abilities of Scaled Quantum Mechanical Molecular Force Fields: Application to 1,3-Butadiene

The positions of some IR bands of the s-trans-1,3-butadiene-h ₆ and -1,1,2-d ₃ isotopomers in the gas phase have been measured using a Brucker IFS 120 HR spectrometer with a resolution of 2 cm^–1. The structural parameters of the s-trans- and s-gauche-1,3-butadiene conformers were optimized completely at the MP2/6-31G* theoretical level and their MP2/6-31G*//MP2/6-31G* quantum mechanical force fields (QMFFs) were calculated. Using only the experimental vibrational frequencies of s-trans-1,3-butadiene-h ₆ the QMFF of the s-trans conformer was corrected by Pulay's scaling method (eight scale factors were involved). The scaled QMFF was used to calculate the mean vibrational amplitudes and the Coriolis coupling constants of s-trans-1,3-butadiene-h ₆ and the vibrational frequencies of 12 of its deuterated isotopomers. The set of scale factors obtained for correction of the s-trans QMFF was transferred to the QMFF of the s-gauche conformer. Its theoretical vibrational spectrum and those of some deuterated and C¹³ isotopomers were calculated. The ability of this scaling approach (transferring of scale factors) to predict the vibrational frequencies of rotational conformers and their isotopomers, as well as other molecular characteristics, and to permit detection of perturbations of the experimental bands are discussed.     

Identification of the high-energy conformer of octa-1,3,5,7-tetraene detected in the one-photon excitation fluorescence spectrum

Scaled quantum-mechanical force field (SQM-FF) vibrational analyses at the HF/6-31G//HF/6-31G computational level of the gauche, Trans,trans,Trans,trans-, gauche,Trans,trans,Cis,trans-, trans,Trans,gauche,Trans,trans-, and trans,Cis,trans,Trans,trans-conformers of octa-1,3,5,7-tetraene were used to identify the rotational isomer observed in the one-photon excitation fluorescence spectrum of this conjugated molecule (Ackerman et al. in J Chem Phys 80:39–44, 1984) as the gauche,Trans,trans,Trans,trans (gTtTt)-conformer. The analysis was performed by comparing the RMS deviations of the 14 fundamental wavenumbers assigned to the high-energy conformer of octa-1,3,5,7-tetraene in the fluorescence spectrum with those calculated for these conformers. Some reassignments of the wavenumbers, originally suggested by experimental observations, were required for the current analysis. The non-planar structure of gTtTt-octa-1,3,5,7-tetraene was calculated to have the terminal –CH=CH₂ moiety rotated by ~30.5° with respect to the remainder of the nearly planar skeleton using both the HF/6-31G and MP2(FC)/aug-cc-pVDZ computational levels. The barriers to rotation of the –CH=CH₂ moiety at the MP2(FC)/aug-cc-pVDZ level were as follows: rotation from the lowest-energy planar all-trans conformer to the non-planar gTtTt-conformer was 31.4 kJ/mol; rotation from the gTtTt-conformer to the planar all-trans conformer was 18.0 kJ/mol; and the barrier between the two equivalent gTtTt-octa-1,3,5,7-tetraene conformers was only 1.4 kJ/mol.     

The effect of electron correlation on the conformational space of melatonin

The pineal gland hormone melatonin regulates several physiological processes including circadian rhythm and also alleviates oxidative stress‐induced degenerative diseases. In spite of its important biological roles, no high level ab initio conformational study has been conducted to reveal its structural features. In this work, the conformational flexibility of melatonin was investigated using correlated ab initio calculations. Conformers, obtained previously at the Hartree‐Fock level (HF/6‐31G*), were fully optimized using second order Møller‐Plesset perturbation theory applying the frozen core approximation (MP2(FC)/6‐31G*). Furthermore, single‐point MP4(SDQ,FC)/6‐31G*//MP2(FC)/6‐31G* computations were performed to investigate the effect of higher order perturbation terms. The HF and MP2 conformational spaces are considerably different: the initial 128 structures converged into 102 different local minima as confirmed by frequency calculations; 28 new minima appeared and 26 previous HF local minima disappeared; no “all‐trans” C3 side chain conformations are seen at the MP2(FC) level. The MP2 global minimum conformation is stabilized by an aromatic‐side chain interaction. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008     

Own N-layered integrated molecular orbital and molecular mechanics study of the reaction of OH<Superscript>−</Superscript> with polychlorinated hydrocarbons CH<Subscript>(4−n)</Subscript>Cl<Subscript>n</Subscript> (n=2–4)

The reliability of the two-layer own N-layered integrated molecular orbital and molecular mechanics (ONIOM) method was examined for the S_N2 reaction CH_(4–n)Cl_n+OH^–. In the ONIOM calculation, only the methyl chloride and OH^–were treated at a high level and the effect of polychlorination was taken into account only at a low level. The ONIOM results were compared with the target CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ results obtained by Borisov etal. [(2001) J. Phys. Chem. A 105:7724]. The ONIOM[MP2/aug-cc-pVDZ:B3LYP/6-31+G(d)] was found to reproduce well the target geometry and energy at the MP2/aug-cc-pVDZ level. The single-point improved energetics at the ONIOM[CCSD(T)/aug-cc-pVDZ:MP2/6-31+G(d)] is found to give results nearly as accurate as the target CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ results. The substantially reduced cost, 20% for optimization and 5% for single-point improved energy of the target cost for n=4, as well as small errors suggest that ONIOM is a powerful tool for accurate potential-energy surfaces of the reaction of large polyhalohydrocarbons.     

An ab initio study of the structure,dissociation energy,and heat of formation of Na2S

The equilibrium geometries and fundamental frequencies of Na₂S are calculated at HF, MP2(FC, FU), and MP3 with the 6–31G(d) basis set and at HF and MP2(FC, FU) with the 6–31G(d) basis set, respectively. The total energy at MP2(FU)/6–31G(d)-optimized geometry is computed at MP4 with 6–311G(d, p), 6–311 + G(d, p), and 6–311G(2df, p), at QCISD(T)/6–311G(d, p), and at MP2/6–311G(3df, 2p) levels, respectively. The dissociation energy, the atomization energy, and the heat of formation for Na₂S are evaluated using the G1 and G2 models. The calculated results indicated that Na₂S in its ground state was a bent structure (C_2v). Electron correlation corrections on the bending angle are very significant. The equilibrium geometrical parameters are R_e(Na-S) = 2.45 Å and ∠Na-S-Na = 111.13° at the MP2(FU)/6–31G(d) level. The theoretically estimated dissociation energy, total atomization energy, and heat of formation are 67.07, 117.55, and 0.35 kcal mol⁻¹, respectively, at 298.15 K. © 1997 John Wiley & Sons, Inc.     

Structural and vibrational analyses of t,C,t,T,t,T,t-deca-1,3,5,7,9-pentaene

An analysis of the results of the fluorescence spectrum investigation of all-trans-deca-1,3,5,7,9-pentaene and t,C,t,T,t,T,t-deca-1,3,5,7,9-pentaene in an n-decane matrix [B.E. Kohler, V. Terpougov, J. Chem. Phys. 108 (1998) 9586–9593] has been performed using scaled quantum mechanical force field (SQM-FF) methodology at the HF/6-31G level. The measured vibronic wavenumbers were assigned taking into account the results of quantum-chemical predictions of the vibrational spectra for all-trans-deca-1,3,5,7,9-pentaene and t,C,t,T,t,T,t-deca-1,3,5,7,9-pentaene. Results from additional calculations at the MP2(FC)/aug-cc-pVDZ and B3LYP/6-311++G(d,p) levels are also reported.     

An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer

Different geometries of nitromethane dimer and nitromethane trimer have been fully optimized employing the density functional theory B3LYP method and the 6-31++G** basis set. Three-body interaction energy has been obtained with the ab initio supermolecular approach at the levels of MP2/6-31++G**//B3LYP/6-31++G** and MP2/aug-cc-pVDZ//B3LYP/6-31++G**. The internal rotation of methyl group induced by intermolecular interaction has been observed theoretically. For the optimized structures of nitromethane dimer, the strength of C--H...O--N H-bond ranges from -9.0 to -12.4 kJ mol(-1) at the MP2/aug-cc-pVDZ//B3LYP/6-31++G** level, and the B3LYP method underestimates the interaction strength compared with the MP2 method, while MP2/6-31++G**//B3LYP/6-31++G** calculated DeltaE(C) is within 2.5 kJ mol(-1) of the corresponding value at the MP4(SDTQ)/6-31G**//B3LYP/6-31++G** level. The analytic atom-atom intermolecular potential has been successfully regressed by using the MP2/6-31++G**//B3LYP/6-31++G** calculated interaction energies of nitromethane dimer. For the optimized structures of nitromethane trimer the three-body interaction energies occupy small percentage of corresponding total binding energies, but become important for the compressed nitromethane explosive. In addition, it has been discovered that the three-body interaction energy in the cyclic nitromethane trimer is more and more negative as intermolecular distances decrease from 2.2 to 1.7 A.     

Effect of basic set quality and electron correlation on the scale factors of a harmonic force field

The completely optimized structure and harmonic force field of s-trans-buta-1,3-diene are reported at the MP2/6-31G and MP2/6-31G* levels of computation. Sets of empirical scale factors for the calculated force fields are derived and compared with the corresponding values computed at the RHF/4-31G and RHF/6-31G levels. Changes in the scale factors for this series of force fields are discussed. The vibrational frequencies are also reported for thirteen isotopomers of s-trans-buta-1,3-diene using the MP2/6-31G* force field. Some characteristics of the gauche and cis forms of buta-1,3-diene are also given.     

Ab initio models for multiple-hydrogen exchange: Comparison of cyclic four- and six-center systems

High-level ab initio calculations {QCISD(T)/6-311 +G**//MP2(fu)/6-31 +G**, with corrections for higher polarization [evaluated at MP2/6-311 +G(3df,2p)] and ΔZPE//MP2(fu)/6-31 +G**, i.e., comparable to Gaussian-2 theory} indicate concerted mechanisms for double- and triple-hydrogen exchange reactions in HF and HCl dimers and trimers, in mixed dimers and trimers containing one NH₃, and in mixed dimers of HF, HCl, and NH₃ with formic acid. All these reactions proceed via cyclic four- or six-center transition structures, the latter being generally more favorable. Calculated activation barriers (ΔH^d? at 0 K, kcal/mol) are 42.3 for (HF)₂, 20.3 for (HF)₃, 41.2 for (HCl)₂, 25.6 for (HCl)₃, 36.0 for NH₃-HF, 10.6 for NH₃(HF)₂, 19.9 for NH₃-HCl, 2.3 for NH₃(HCl)₂, 9.7 for HCO₂H-HF, 7.0 for HCO₂H-HCl, and 11.3, for HCO₂H-NH₃. The barriers are lower for the more ionic systems and when more ion pair character is present. © John Wiley & Sons, Inc.     

The photoelectron spectrum and conformation of phenylphosphine and phenylarsine

He(I) and He(II) photoelectron spectra of phenylphosphine and phenylarsine have been investigated and assigned. The rotational barrier of the phosphino group has been investigated at the MP2/6-31G(d,p)//MP2/6-31G(d,p) and HF/6-31G(d,p)//HF/6-31G(d,p) levels of theory, and that of the arsino group at the HF/6-31G(d,p)//6-31G(d,p) levels of theory. The rotational barrier of the two molecules is nearly the same. The energy difference between the two possible conformers of the molecules is low (1.5 kJ/mol at the MP2/6-31G(d,p) level of theory), allowing nearly free rotation about the P-C bond. The photoelectron spectrum cannot be interpreted by considering the most stable rotamer, but all possible conformers should be taken into account. The present interpretation is consistent with the smalln _p - interaction concluded from other investigations. The rotational barrier ofo-phosphinophenol is significantly larger than for phenylphosphine, and the photoelectron spectrum of this compound can be interpreted by considering a single conformer, and no appreciable interaction between the -system of the ring and the phosphorus lone pair.     

Mechanistic aspects of the abstraction of an allylic hydrogen in the chlorine atom reaction with 2-methyl-1,3-butadiene (isoprene)

The different channels for the abstraction of an allylic hydrogen in the chlorine atom reaction with isoprene were explored using ab initio methodology. It is shown that the metathesis reaction proceeds through an association-elimination mechanism in which a weakly bound intermediate (HCl.C(5)H(7)(*)) is formed first (formal addition). Further evolution by HCl elimination leads to the final C(5)H(7)(*) radical. QCISD(T)/aug-cc-pVDZ//MP2/6-31G(d,p) calculations show that for two of the possible pathways the barrier heights involved are moderate and the formation of the intermediates are exergonic (DeltaG < 0). Therefore, the mechanism proposed is both kinetically and thermodynamically feasible. The pressure dependence experimentally observed for the Cl + isoprene reaction can be rationalized in terms of the association-elimination mechanism proposed.     

几种含芯电子相关能修正的G2和G2(ACI)方法

针对冻结芯电子近似,在MP2/6-311G(d,p)级别上对G2、MP2/6-311G(d)和MP2/6-311G(d,p)级别上对G2(QCI)方法进一步考虑了芯电子相关能修正,尝试建立了G2(fu2)、G2(QCI/ful)和G2(QCI/fu2)方法。G2-l test set 的反应能量计算结果表明,这些方法进一步减小了经验修正量;G2(QCI/ful)和G2(QCI/fu2)也比G2(QCI)的总体精度有所提高;但G2(fu2)在G2基础上,总体精度没有改善。G2(fu2)、G2(QCI/ful)和G2(QCI/fu2)计算G2-l test set反应能量的平均绝对偏差分别为5.11、4.74和4.81kJ mol-1,G2和G2(QCI)分别为5.09和4.97kJ mol-1.     

Proton affinities of molecules containing nitrogen and oxygen: comparing ab initio and semiempirical results to experiments

We report a comparison of theoretical and experimental proton affinities at nitrogen and oxygen sites within a series of small molecules. The calculated proton affinities are determined using the semiempirical methods AM 1, MNDO , and PM 3; the ab initio Hartree–Fock method at the following basis levels: 3-21G //3-21G , 3-21+G //3-21G , 6-31G *//6-31G *, and 6-31+G (d, p)//6-31G *; and Møller–Plesset perturbation calculations: MP 2/6-31G *//6-31G *, MP 3/6-31G *//6-31G *, MP 2/6-31G +(d, p)//6-31G *, MP 3/6-31G +(d, p)//6-31G *, and MP 4(SDTQ )/6-31G +G (d, p)//6-31G *. The semiempirical methods have more nonsystematic scatter from the experimental values, compared to even the minimal 3-21G level ab initio calculations. The thermodynamically corrected 6-31G *//6-31G * proton affinities provide acceptable results compared to experiment, and we see no significant improvement over 6-31G *//6-31G * in the proton affinities with any of the higher-level calculations. © 1992 John Wiley & Sons, Inc.     

AB initio study of thermodynamic stability and structure of cage molecules B4N4H8 and Be4O4H8

Stable molecular structures of heterocubane systems B₄N₄H₈ 2 and Be₄O₄H₈, isoelectronic to the cubane molecule, are investigated by ab initio (RHF/6-31G**, MP2(full)/6-31C**, and MP2(full)/6-311+ + G**) methods and are shown to be highly thetmodynamically stable. Decomposition of structure 2 into two 1,3,2,4-diazadiboroethidine molecules 6 or four iminobomne NBNH molecules 11 is an endothermal process taking 10.1 (RHF/6-31G**), 39.6 (MP2(full)/6-31G**) kcaUmole and 140.6 (RHF/6-31G**), 161.4 (MP2(full)/6-31G**) kcal/mole, respectively. Decomposition of structure 3 into two 1,3,2,4-dioxydi-beryllothidine molecules 12 or four molecules 13 is also an endothermal reaction taking 22.1 (RHF/6-31G**), 39.8 (MP2(full)/6-31G**) kcal/mole and 127.1 (RHF/6-31G**), 155.2 (MP2(full)/631G**) kcal/mole, respectively. The geometrical characteristics of simple molecules BeH₂ 15, Be₂ 16 and 17, Be₂H₂ 18, Be₂H₄ 19, BeO 20, and Be₂O₂ 21 are calculated. Translated from Zhumal Struktumoi Khim ii, Vol. 41, No. 1, pp. 3-13, January–February, 2000     

Theoretical approach to the mechanism of reactions between halogen atoms and unsaturated hydrocarbons: the Cl + propene reaction

The potential energy surface for the Cl + propene reaction was analyzed at the MP2 level using Pople's 6-31G(d,p) and 6-311+G(d,p), and Dunning's cc-pVDZ and aug-cc-pVDZ basis sets. Two different channels for the addition reaction leading to chloroalkyl radicals and five alternative channels for the abstraction reaction leading to C(3)H(5) (.) + HCl were explored. The corresponding energy profiles were computed at the QCISD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ level of theory. Theoretical results suggest that the previously established mechanism consisting of (1) direct abstraction and (2) addition-elimination steps is instead made up of (1) addition through an intermediate and (2) two-step abstraction processes. No direct abstraction mechanism exists on the potential energy surface. The kinetic equations derived for the new mechanism are consistent with the pressure dependence experimentally observed for this reaction.     

New insights into an old reaction. High-resolution x-ray powder diffraction of Wiberg's aminoalane intermediate

In accordance with the procedure described by E. Wiberg, Me(3)Al-NH(3) was heated as a bulk material in inert atmosphere to give a colorless liquid which slowly loses methane. Close to the end of this elimination reaction, the melt crystallized to give a microcrystalline powder of (Me(2)AlNH(2))(x)(). The structure of this intermediate has been solved by the method of high-resolution X-ray powder diffraction. The compound crystallizes in the monoclinic space group C2/c with the cell parameters of a = 15.0047(6) A, b = 8.7500(2) A, c = 24.4702(8) A, and beta = 107.290(2) degrees, with eight trimers (Me(2)AlNH(2))(3) per unit cell. These trimers crystallize in a boat conformation in contrast to the known trimers of the same composition where a twist-boat conformation had been found by single crystal determination. Different conformers of (Me(2)AlNH(2))(3) have been investigated by theoretical methods (HF/6-31G(d), B3LYP/6-31G(d), B3LYP/6-311G(d,p), MP2(fc)/6-31G(d), and MP2(fc)/6-311G(d,p)). The twist-boat and the chair conformer correspond to minima at the potential energy surface, whereas the boat conformer corresponds to a first-order transition state (relative energies of 0.45-2.56 kJ/mol (boat) and 6.66-11.91 kJ/mol (chair)). Relaxed scans of the potential energy surface at the HF/6-31G(d) and B3LYP/6-31G(d) levels have shown that the boat conformer (C(s)() symmetry) connects two enantiomers of the twist-boat form (C(2) symmetry).     

Hydrogen peroxide clusters: the role of open book motif in cage and helical structures

Hartree-Fock (HF) calculations using 6-31G*, 6-311++G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets show that hydrogen peroxide molecular clusters tend to form hydrogen-bonded cyclic and cage structures along the lines expected of a molecule which can act as a proton donor as well as an acceptor. These results are reiterated by density functional theoretic (DFT) calculations with B3LYP parametrization and also by second-order M?ller-Plesset perturbation (MP2) theory using 6-31G* and 6-311++G(d,p) basis sets. Trends in stabilization energies and geometrical parameters obtained at the HF level using 6-311++G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets are similar to those obtained from HF/6-31G* calculation. In addition, the HF calculations suggest the formation of stable helical structures for larger clusters, provided the neighbors form an open book structure.     

Ab initio study of the conformational equilibrium of ethylene glycol

Summary The conformational equilibrium of ethylene glycol (CH₂OHCH₂OH) has been examined by performing geometry optimizations at the 6-31G*, MP2/6-31G* and 6-31G** levels. Final energies have been calculated at the MP3 level with the optimized geometries. The two most stable conformers are atGg andgGg but it is verified that the inclusion of electronic correlations reduces their energy difference of 0.6 kcal/mol at the HF level to less than 0.2 kcal/mol. The possible coexistence of the two most stable conformers is in agreement with some previous studies of Frei et al. For thetXg conformer a detailed analysis of the intramolecular potential as a function of rotation around the C-C bond is also reported.