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Mixed quantum mechanics/molecular mechanics (QM/MM) techniques are used for exploring several feasible low-energy pathways of the nucleotide transfer reaction of pol [beta] for correct G:C basepairing versus the incorrect G:G case. The results have helped in interpreting the nucleotide specificity differences across polymerase families in terms of the concept of active site preorganization.

The molecular structures of gaseous CH3AsF2 and (CH3)2AsF were determined by electron-diffraction experiments and ab initio computations. Findings indicated that both As-C and As-F bond lengths are shortened by increasing numbers of fluorine atoms but that the angles CAsF and FAsF are almost invariant in the series (CH3)3As, (CH3)2AsF, CH3AsF2, and AsF3.

A study has been conducted to examine the structure of perfluorocyclopropene, a perfluorinated compound, in gaseous, solution and crystalline states using electron diffraction, rotational spectroscopy and liquid crystal NMR spectroscopy, respectively. X-ray diffraction techniques were also used to measure crystal growth. The structural parameters for the solid and gas phases are presented.

Electron diffraction, ab initio and IGLO computations analyze the molecular structure of 1-(difluoroboryl)pentaborane(9), demonstrating high thermal stability in the gas phase. A difluoroboryl group replaced the apical boron atom of the molecule, which comprised a pentaborane(9) cage. The exo B-B bond was the center of rotation for the BF2 moiety.

An analysis of the C-C ring opening reaction of the oxirane molecule on the singlet potential energy surface, in the context of ab initio electronic structure theory, identified three minima on the surface relating to the closed-shell ring structure (as reactant), and two closed-shell open structure (as products) of C2 and Cs symmetry. Four authentic transition states on the associated reaction coordinates connect these minima.

An investigation concerning nine electronically low-lying doublet states of the SNS molecule appeared recently. The present paper represents the conclusion of studies on the NS2 molecule, focusing on the low-lying SNS quartet states. Nine quartet states, including six bent structures (4A2, 4B2, two 4A1, and two 4B1 ) and three linear structures (4Πg and two 4Πu ), have been investigated at the self-consistent field (SCF), single and double excitation configuration interaction (CISD), and complete active space (CAS) SCF levels of theory with five basis sets, double zeta (DZ) through triple zeta plus double polarization (TZ+2P). Four of these quartet states lie within 1.8 eV (42.0 kcal mol-1 ) of the 2A1 ground state of NS2. Thus one or more of these quartet states (which lie much lower than for the valence isoelectronic NO2 molecule) should be observable. At the SCF level of theory the stability of the wave functions and the relative energies of the nine quartet states are discussed in conjunction with the molecular orbital (MO) Hessian. [ABSTRACT FROM AUTHOR]

The ground state of the SiC3 molecule is found to be a closed-shell cyclic C2v symmetry structure which can be described as a four-membered ring with a transannular (cross ring) carbon–carbon bond, r(C–C)=1.469 Å. Theoretical studies with a triple-zeta plus double-polarization function (TZ2P) basis set in conjunction with the configuration-interaction technique at the TZ2P self-consistent-field optimized geometries predict this rhomboidal structure to be 4.1 kcal/mol more stable than the linear triplet Si–C–C–C isomer. A second closed-shell rhomboidal C2v symmetry structure with carbon–silicon transannular bonding, r(Si–C)=1.880 Å, was located and characterized as a local minimum lying 4.3 kcal/mol above the ground-state rhomboidal structure at this level of theory. Higher-level theoretical methods, including contributions from triple excitations, with larger basis sets will be required to obtain a more definitive set of relative energies. [ABSTRACT FROM AUTHOR]

The value of the Mo\ller–Plesset third order calculations is examined. An efficient method for the evaluation of the gradient of the MP3 energy is reported, and it has been programmed for both restricted and unrestricted Hartree–Fock wave functions. Large basis set calculations (TZ2P or better) are reported for the optimization of geometries and the determination of harmonic frequencies (which are obtained by finite differences of analytic gradients). The molecules selected are NH2, PH2, AsH2, H2O, NH3, H2CO, HCN, and C2H2. For the closed shell systems, the RMP3 predictions for bond lengths are inferior (approx. 0.006 Å) to RMP2 predictions (approx. 0.003 Å) for single bonds, and for multiple bonds the RMP3 bond lengths are too short by approximately the same amount (approx. 0.01 Å) that RMP2 are too long. For the open shell systems, the UMP3 geometrical parameters show only a marginal improvement over UMP2, except for PH2 where the bond length error is reduced to 0.003 Å. The results for harmonic frequencies show a similar comparison between MP2 and MP3. On the basis of this experience, it appears that large scale calculations at the MP3 level are not recommended; MP2 calculations with a large basis set are much cheaper and provide results with a similar, if not superior, accuracy. [ABSTRACT FROM AUTHOR]

Minima on the potential energy surfaces of (C2H2)2, (C2H2)3, and (C2H4)2 have been located by ab initio methods, using the Mo\ller–Plesset second-order (MP2) procedure, with a DZP basis set. For (C2H2)2, a T-shaped structure is predicted and for (C2H2)3, a C3h structure. For (C2H4)2 there are two candidates, a T-shaped structure and a staggered-parallel structure, and it is difficult to distinguish between them. Other stationary points have been located on the surfaces, but they are all found to be transition states, by the method of analytic second derivatives. Existing experimental data is insufficient to decide unequivocally as to the geometry of the minima. These calculations appear to resolve these questions and there is no contradiction with the data. [ABSTRACT FROM AUTHOR]

A simple procedure utilizing the molecular orbital (MO) Hessian, the second derivative of the Hartree–Fock (HF) energy with respect to MO coefficient perturbations, has been proposed in the interpretation of anomalous analytic HF energy derivatives. The nature of the anomalous analytic self-consistent field (SCF) harmonic vibrational frequencies and infrared (ir) intensities of the 2B2 and 2A2 excited states of NO2 and HCO2 have been studied in detail. By suitable partitioning of the HF second energy derivative expression, an association between the abnormal force constants, the dipole moment derivatives, and specific solutions to the SCF coupled perturbed HF equations is established. This connection to unstable wave functions can now be used with the MO Hessian to predict these anomalies at the HF level. In addition, appropriate small complete active space SCF (CASSCF) methods have been utilized to overcome the inherent shortcomings of the HF wave functions, and determine more realistic values for the force constants and ir intensities. [ABSTRACT FROM AUTHOR]

The present study aims to characterize the electronically low-lying doublet states of the SNS molecule in detail. From an analysis of the eigenvalues and eigenvectors of the molecular orbital (MO) Hessian at the self-consistent-field (SCF) level, the corresponding rotations amongst the high-lying occupied and low-lying unoccupied molecular orbitals highlight nine low-lying doublet states worthy of study. Three bent (2A1, 2B2, and 2A2), three ring (2B1, 2A2, and 2A1), and three linear (2Πu and two 2Πg) structural isomers with doublet electronic states have been investigated at the SCF, configuration interaction with single and double excitations (CISD), and complete active space (CAS) SCF levels of theory with five different basis sets, double zeta (DZ) through triple zeta plus double polarization (TZ+2P). At the SCF level of theory, the stability of the wave functions and the energetics of the above mentioned doublet states are discussed in terms of the molecular orbital (MO) Hessian. The MO Hessian is often shown to properly predict the energetic ordering of the different electronic states. [ABSTRACT FROM AUTHOR]