Benchmark calculations

Woon D E 1994 Benchmark calculations with correlated molecular wavefunctions. 5. The determination of accurate ab initio intermolecular potentials for He2, Ne2, and A 2 J. Chem. Phys. 100 2838... 

Day P N and Truhlar D G 1991 Benchmark calculations of thermal reaction rates. II. Direct calculation of the flux autocorrelation function for a canonical ensemble J. Chem. Phys. 94 2045-56... 

Schwerdtfeger, P. (1991) Relativistic and Electron Correlation Contributions in Atomic and Molecular Properties. Benchmark Calculations on Au and Au2. Chemical Physics Letters, 183, 457 163. Neogrady, P., Kello, V., Urban, M. and Sadlej, A.J. (1997) Ionization Potentials and Electron Affinities of Cu, Ag, and Au Electron Correlation and Relativistic Effects. International Journal of Quantum Chemistry, 63, 557-565. 

Schipper, P. R. T., Gritsenko, O. V., Baerends, E. J., 1999, Benchmark Calculations of Chemical Reactions in Density Functional Theory Comparison of the Accurate Kohn-Sham Solution With Generalized Gradient Approximations for the H2+H and H2+H2 Reactions , J. Chem. Phys., Ill, 4056. 

To illustrate the potential of the three-layer ONIOM method, we show results from a systematic comparison of three- and two-layer ONIOM methods with full QM benchmark calculations [11], The system studied is a zwitterionic peptide, NH3+—CHnBu—CO—NH—CH2—CO—NH—CH Bu—COO-, and the partition scheme illustrated in Figure 2-2 is used. In this partition, both model and mid... 

Although water structure and sidechain flexibilities are useful gauges for the simulation protocol, more quantitative measures are needed for reliable QM/MM simulations of enzyme systems. In this regards, we have found that reduction potential [78] and pKa [73,91] calculations are particularly useful benchmark calculations because the results are likely very sensitive to the simulation details. 

Warshel is to utilize a formula identical to (11.22) in this chapter to compute the free energy change. They employed an empirical valence bond (EVB, below) approach to approximately model electronic effects, and the calculations included the full experimental structure of carbonic anhydrase. An H/D isotope effect of 3.9 1.0 was obtained in the calculation, which compared favorably with the experimental value of 3.8. This benchmark calculation gives optimism that quantum effects on free energies can be realistically modeled for complex biochemical systems. 

The standard enthalpy of this reaction is equal to the difference PA(K) — PA(B). Thus, the determination of PA(K) requires PA B). The proton affinity of B will rely, in turn, on the proton affinity of some other molecule and so on. A scale of relative values of proton affinities is thus built. To derive absolute data, a reliable anchor must be found. The one most frequently used is the proton affinity of ammonia, /M(NH3), which is now accepted to be 853.6 kJ mol-1 [67]. This is in excellent agreement with the result of a benchmark calculation by Martin and Lee,P (NH3) = 853.1 1.3 kJmol-1 [70],... 

Our philosophy was instead top-down . We decomposed the molecular TAE (total atomization energy TAEe at the bottom of the well, TAEo at absolute zero) into all components that can reasonably affect it at the kl/mol level. Then we carried out exhaustive benchmark calculations on each component separately for a representative training set of molecules. Finally, for each component separately, we progressively introduced approximations up to the point where reproduction of that particular component started deteriorating to an unacceptable extent. Thus, experimental data entered the picture only at the validation stage, not at the design stage. 

Benchmark calculations of the equilibrium atomization energies (AEs) of the small molecules CH2, H2O, HF, N2, CO and F2 are presented in Table II. The CCSD(T) calculations are performed in systematically increasing correlation-... 

It has been demonstrated in several benchmark calculations that the CR-CCSD(T) (completely renormalized CCSD(T)) and CR-CCSD(TQ) (completely renormalized CCSD(TQ)) methods provide an excellent description of entire PESs involving single and double bond dissociation (P, 13, 15, 17-19, 21, 111), highly-excited vibrational term values near dissociation 17, 18, 21, 111), and... 

In the present work, correlation consistent basis sets have been developed for the transition metal atoms Y and Hg using small-core quasirelativistic PPs, i.e., the ns and (nA)d valence electrons as well as the outer-core (nA)sp electrons are explicitly included in the calculations. This can greatly reduce the errors due to the PP approximation, and in particular the pseudo-orbitals in the valence region retain some nodal structure. Series of basis sets from double-through quintuple-zeta have been developed and are denoted as cc-pVwZ-PP (correlation consistent polarized valence with pseudopotentials). The methodology used in this work is described in Sec. II, while molecular benchmark calculations on YC, HgH, and Hg2 are given in Sec. III. Lastly, the results are summarized in Sec. IV. 

The recent versions of the slow motion approach were applied to direct fitting of experimental data for a series of Ni(II) complexes of varying symmetry (97). An example of an experimental data set and a fitted curve is shown in Fig. 9. Another application of the slow-motion approach is to provide benchmark calculations against which more approximate theoretical tools can be tested. As an example of work of this kind, we wish to mention the paper by Kowalewski et al. (98), studying the electron spin relaxation effects in the vicinity and beyond the Redfield limit. 

Crump KS, Gibbs JP (2005) Benchmark calculations for perchlorate from three human cohorts. Environ Health Perspect 113 1001-1008... 

Crump, K.S. 1984. A new method for determining aUowable daily intakes. Fundam. Appl. Toxicol. 4 854-871. Crump, K. 2002. Critical issues in benchmark calculations from continuous data. Crit. Rev. Toxicol. 32 133-153. 

Fig. 2. This figure shows the electronic energy of the ground state of H2 molecule, calculated in a crude approximation using only one configuration. The benchmark calculation of Kolos and Wolniewicz is exhibited for comparison. Accuracy can be seen to be improved by using more atomic orbitals even when a rough approximation is used for the interelectron repulsion matrix element.

Benchmark Calculations for Molecular Systems—Energy and Geometry... 

Benchmark Calculations for Molecular Systems—Vibrational Frequencies... 

Finally the BERTHA technology has been applied to relativistic density functional theory by Quiney and Belanzoni [36]. This showed that the method works well for closed shell atoms as compared with benchmark calculations using finite difference methods, and there have been promising parallelization studies [37] which should in future greatly extend the range of application of the code. 

All molecules will show an MCD spectrum. The spectrum of many types of molecule can now be simulated, often through more than one theoretical approach. Several areas need further study however. It would be useful if all types of MCD spectrum could be calculated at a range of levels of theory so that a scientist interested in predicting a spectrum would be able to choose an approach that suitably fits their needs. More benchmark calculations are needed to improve our understanding of the limitations of the present methods. These calculations would be aided by the availability of more high-quality spectra of small molecules that would be suitable test cases. While the MCD spectra of many molecules can now be calculated, one area that probably still cannot be studied with confidence is paramagnetic molecules that include very heavy elements. In this case spin-orbit effects will be very large and perturbational treatments like those applied thus far are unlikely to provide accurate results. 

---