A detailed analysis of pseudorotation in PH4F

Summary Pentacoordinated molecules are thought to undergo intramolecular isomerization by the widely accepted Berry pseudorotation mechanism. Through our investigations, we have found that the actual pseudorotation for the PH₄F system is more complex than that envisioned by Berry. The potential energy surface of PH₄F is mapped out at the RHF/6-311G(d, p) level. According to the Berry mechanism, this system is expected to have two minima and two maxima; however, the system actually has two transition states and one global minimum. The minimum energy path from the highest transition state is followed to the second transition state, which in turn has a minimum energy path leading to the global minimum. Along the path between the two transition states there is a branching region. This portion of the potential energy surface is probed extensively.Dedicated to Prof. Klaus Ruedenberg     

Singlet and triplet potential surfaces for the O2+C2H4 reaction

Electronic structure calculations at the CASSCF and UB3LYP levels of theory with the aug-cc-pVDZ basis set were used to characterize structures, vibrational frequencies, and energies for stationary points on the ground state triplet and singlet O(2)+C(2)H(4) potential energy surfaces (PESs). Spin-orbit couplings between the PESs were calculated using state averaged CASSCF wave functions. More accurate energies were obtained for the CASSCF structures with the MRMP2/aug-cc-pVDZ method. An important and necessary aspect of the calculations was the need to use different CASSCF active spaces for the different reaction paths on the investigated PESs. The CASSCF calculations focused on O(2)+C(2)H(4) addition to form the C(2)H(4)O(2) biradical on the triplet and singlet surfaces, and isomerization reaction paths ensuing from this biradical. The triplet and singlet C(2)H(4)O(2) biradicals are very similar in structure, primarily differing in their C-C-O-O dihedral angles. The MRMP2 values for the O(2)+C(2)H(4)→C(2)H(4)O(2) barrier to form the biradical are 33.8 and 6.1 kcal/mol, respectively, for the triplet and singlet surfaces. On the singlet surface, C(2)H(4)O(2) isomerizes to dioxetane and ethane-peroxide with MRMP2 barriers of 7.8 and 21.3 kcal/mol. A more exhaustive search of reaction paths was made for the singlet surface using the UB3LYP/aug-cc-pVDZ theory. The triplet and singlet surfaces cross between the structures for the O(2)+C(2)H(4) addition transition states and the biradical intermediates. Trapping in the triplet biradical intermediate, following (3)O(2)+C(2)H(4) addition, is expected to enhance triplet→singlet intersystem crossing.     

Ab initio and analytic intermolecular potentials for Ar-CH(3)OH

Ab initio calculations at the CCSD(T)/aug-cc-pVTZ level of theory were used to characterize the Ar-CH(3)OH intermolecular potential energy surface (PES). Potential energy curves were calculated for four different Ar + CH(3)OH orientations and used to derive an analytic function for the intermolecular PES. A sum of Ar-C, Ar-O, Ar-H(C), and Ar-H(O) two-body potentials gives an excellent fit to these potential energy curves up to 100 kcal mol(-1), and adding an additional r(-n) term to the Buckingham two-body potential results in only a minor improvement in the fit. Three Ar-CH(3)OH van der Waals minima were found from the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ calculations. The structure of the global minimum is in overall good agreement with experiment (X.-C. Tan, L. Sun and R. L. Kuczkowski, J. Mol. Spectrosc., 1995, 171, 248). It is T-shaped with the hydroxyl H-atom syn with respect to Ar. Extrapolated to the complete basis set (CBS) limit, the global minimum has a well depth of 0.72 kcal mol(-1) with basis set superposition error (BSSE) correction. The aug-cc-pVTZ basis set gives a well depth only 0.10 kcal mol(-1) smaller than this value. The well depths of the other two minima are within 0.16 kcal mol(-1) of the global minimum. The analytic Ar-CH(3)OH intermolecular potential also identifies these three minima as the only van der Waals minima and the structures predicted by the analytic potential are similar to the ab initio structures. The analytic potential identifies the same global minimum and the predicted well depths for the minima are within 0.05 kcal mol(-1) of the ab initio values. Combining this Ar-CH(3)OH intermolecular potential with a potential for a OH-terminated alkylthiolate self-assembled monolayer surface (i.e., HO-SAM) provides a potential to model Ar + HO-SAM collisions.     

A parallel distributed data CPHF algorithm for analytic Hessians

One of the most commonly used means to characterize potential energy surfaces of reactions and chemical systems is the Hessian calculation, whose analytic evaluation is computationally and memory demanding. A new scalable distributed data analytic Hessian algorithm is presented. Features of the distributed data parallel coupled perturbed Hartree-Fock (CPHF) are (a) columns of density-like and Fock-like matrices are distributed among processors, (b) an efficient static load balancing scheme achieves good work load distribution among the processors, (c) network communication time is minimized, and (d) numerous performance improvements in analytic Hessian steps are made. As a result, the new code has good performance which is demonstrated on large biological systems.     

O?+?C2H4 potential energy surface: lowest-lying singlet at the multireference level

Extensive density functional theory (DFT) calculations have been performed to develop a force field for the classical molecular dynamics (MD) simulations of various azobenzene derivatives. Besides azobenzene, we focused on a thiolated azobenzene’s molecular rod (4′-{[(1,1′-biphenyl)-4-yl]diazenyl}-(1,1′-biphenyl)-4-thiol) that has been previously demonstrated to photoisomerize from trans to cis with high yields on surfaces. The developed force field is an extension of OPLS All Atoms, and key bonding parameters are parameterized to reproduce the potential energy profiles calculated by DFT. For each of the parameterized molecule, we propose three sets of parameters: one best suited for the trans configuration, one for the cis configuration, and finally, a set able to describe both at a satisfactory degree. The quality of the derived parameters is evaluated by comparing with structural and vibrational experimental data. The developed force field opens the way to the classical MD simulations of self-assembled monolayers (SAMs) of azobenzene’s molecular rods, as well as to the quantum mechanics/molecular mechanics study of photoisomerization in SAMs.     

Parallel algorithm for integral transformations and GUGA MCSCF

Summary An algorithm for the parallelization of the atomic to molecular integral transformation and the subsequent steps in a GUGA based MCSCF calculation is presented. Timing data shows that the transformation and diagonalization steps are well parallelized and that several of the other portions of the MCSCF code are moderately parallel. Remaining sequential bottlenecks are identified.     

Effect of the Ar-Ni(s) potential on the cross section for Ar+CH4/Ni{111} collision-induced desorption and the need for a more accurate CH4/Ni{111} potential

In a previous paper [L. Sun, P. de Sainte Claire, O. Meroueh, and W. L Hase, J. Chem. Phys. 114, 535 (2001)], a classical trajectory simulation was reported of CH(4) desorption from Ni{111} by Ar-atom collisions. At an incident angle theta(i) of 60 degrees (with respect to the surface normal), the calculated collision-induced desorption (CID) cross sections are in excellent agreement with experiment. However, for smaller incident angles the calculated cross sections are larger than the experimental values and for normal collisions, theta(i)=0 degrees , the calculated cross sections are approximately a factor of 2 larger. This trajectory study used an analytic function for the Ar+Ni(s) intermolecular potential which gives an Ar-Ni{111} potential energy minimum which is an order of magnitude too deep. In the work reported here, the previous trajectory study is repeated with an Ar+Ni(s) analytic intermolecular potential which gives an accurate Ar-Ni{111} potential energy minimum and also has a different surface corrugation than the previous potential. Though there are significant differences between the two Ar+Ni(s) analytic potentials, they have no important effects on the CID dynamics and the cross sections reported here are nearly identical to the previous values. Zero-point energy motions of the surface and the CH(4)-Ni(s) intermolecular modes are considered in the simulation and they are found to have a negligible effect on the CID cross sections. Calculations of the intermolecular potential between CH(4) and a Ni atom, at various levels of theory, suggest that there are substantial approximations in the ab initio calculation used to develop the CH(4)+Ni{111} potential. The implication is that the differences between the trajectory and experimental CID cross sections may arise from an inaccurate CH(4)+Ni{111} potential used in the trajectory simulation.     

Yuri Alexeev,Theresa L. Windus,Chang‐Guo Zhan,David A. Dixon,Erratum to “Accurate heats of formation and acidities for H3PO4, H2SO4, and H2CO3 from ab initio electronic structure calculations,” International Journal of Quantum Chemistry (2005) 102(5) 775–784

The original article to which this Erratum refers was published in International Journal of Quantum Chemistry (2005) 102(5) 775–784     

Direct dynamics simulations using Hessian-based predictor-corrector integration algorithms

In previous research [J. Chem. Phys. 111, 3800 (1999)] a Hessian-based integration algorithm was derived for performing direct dynamics simulations. In the work presented here, improvements to this algorithm are described. The algorithm has a predictor step based on a local second-order Taylor expansion of the potential in Cartesian coordinates, within a trust radius, and a fifth-order correction to this predicted trajectory. The current algorithm determines the predicted trajectory in Cartesian coordinates, instead of the instantaneous normal mode coordinates used previously, to ensure angular momentum conservation. For the previous algorithm the corrected step was evaluated in rotated Cartesian coordinates. Since the local potential expanded in Cartesian coordinates is not invariant to rotation, the constants of motion are not necessarily conserved during the corrector step. An approximate correction to this shortcoming was made by projecting translation and rotation out of the rotated coordinates. For the current algorithm unrotated Cartesian coordinates are used for the corrected step to assure the constants of motion are conserved. An algorithm is proposed for updating the trust radius to enhance the accuracy and efficiency of the numerical integration. This modified Hessian-based integration algorithm, with its new components, has been implemented into the VENUS/NWChem software package and compared with the velocity-Verlet algorithm for the H(2)CO-->H(2)+CO, O(3)+C(3)H(6), and F(-)+CH(3)OOH chemical reactions.