Journal of Computational Chemistry

Cossi, Maurizio; Rega, Nadia; Scalmani, Giovanni; Barone, Vincenzo

doi: 10.1002/jcc.10189pmid: 12666158

The conductor‐like solvation model, as developed in the framework of the polarizable continuum model (PCM), has been reformulated and newly implemented in order to compute energies, geometric structures, harmonic frequencies, and electronic properties in solution for any chemical system that can be studied in vacuo. Particular attention is devoted to large systems requiring suitable iterative algorithms to compute the solvation charges: the fast multipole method (FMM) has been extensively used to ensure a linear scaling of the computational times with the size of the solute. A number of test applications are presented to evaluate the performances of the method. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 669–681, 2003

Bosch, David; Campillo, Mercedes; Pardo, Leonardo

doi: 10.1002/jcc.10200pmid: 12666159

The structural and energetic determinants for kinking a basepair step by minor groove–insertion of the protein side chains of PurR, LacI, LEF–1, IHF, Sac7d, and Sso7d, have been calculated by molecular dynamics/potential of mean force simulations. The structural determinants of the kinked structures are: two contiguous furanose rings achieve different conformations, in the region of C3′endo (A–DNA) and C2′endo (B–DNA); the χ torsion angle always takes values characteristic of the C2′endo conformation of B–DNA, independently of sugar puckering; and protein side chain insertion increases slide (from negative to positive values), rise, and roll, and decreases twist. The energetic determinants of DNA kinking are: the conformational transition of the sugar–phosphate backbone is not energetically demanding; the relative importance of the interbase parameters in the free energy penalty is slide, followed by twist and rise, and concluding with shift and roll; and the characteristic increase of roll and decrease of twist, upon side chain insertion, tends to stabilize the process of DNA kinking. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 682–691, 2003

Zyubin, A. S.; Mebel, A. M.

doi: 10.1002/jcc.10220pmid: 12666160

Time‐dependent density functional (TD‐DFT) and perturbation theory‐based outer valence Green functions (OVGF) methods have been tested for calculations of excitation energies for a set of radicals, molecules, and model clusters simulating points defects in silica. The results show that the TD‐DFT approach may give unreliable results not only for diffuse Rydberg states, but also for electronic states involving transitions between MOs localized in two remote from each other spatial regions, for example, for charge‐transfer excitations. For the · O—SiX3 clusters, where X is a single‐valence group, TD‐DFT predicts reasonable excitation energies but incorrect sequence of electronic transitions. For a number of cases where TD‐DFT is shown to be unreliable, the OVGF approach can provide better estimates of excitation energies, but this method also is not expected to perform universally well. The OVGF performance is demonstrated to be satisfactory for excitations with predominantly single‐determinant wave functions where the deviations of the calculated energies from experiment should not exceed 0.1–0.3 eV. However, for more complicated transitions involving multiple bonds or for excited states with multireference wave functions the OVGF approach is less reliable and error in the computed energies can reach 0.5–1 eV. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 692–700, 2003

Masgrau, Laura; González–Lafont, Àngels; Lluch, José M.

doi: 10.1002/jcc.10191pmid: 12666161

The title reaction has been used as an example to test the importance of using a hindered rotor treatment instead of a harmonic oscillator model for calculating vibrational partition functions corresponding to low‐frequency internal rotation modes. First, a normal‐mode analysis according to the Ayala and Schlegel's algorithm has been used to identify the internal rotation modes of methanethiol and the transition state structure. Then, after calculation of the energy barrier for each internal rotation, the corresponding hindered rotor partition functions have been calculated following the CW scheme of Chuang and Truhlar. The results show that the anharmonic treatment produces a rather modest improvement of the rate constants at room temperature or below. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 701–706, 2003

Lorenzo, Luis; Mosquera, Ricardo A.

doi: 10.1002/jcc.10192pmid: 12666162

A box‐counting‐based algorithm (SEBC) has been developed for the numerical computation of the Shannon entropy from samples of continuous functions. Its performance was tested by applying it to several samples of known continuous distribution functions. The results obtained with SEBC reproduced those obtained by analytical or numerical integration. SEBC was also employed for computing the Shannon entropies of the steric energy, Sh(ES), of several amino acids from their in vacuo NVE molecular dynamics simulations using the AMBER‐4 force field. The results obtained correlate linearly with the experimental standard thermodynamic entropies of these compounds. This work points to the possibility of introducing straightforward and reliable calculations of thermodynamic entropies from empirical linear relationships with Sh(ES) obtained from MD simulations. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 707–713, 2003

Koslowski, Axel; Beck, Michael E.; Thiel, Walter

doi: 10.1002/jcc.10210pmid: 12666163

The graphical unitary group approach has been applied in an efficient implementation of a general multireference configuration interaction (MRCI) method for use with small active molecular orbital spaces in a semiempirical framework. Gradients can be computed analytically for molecular orbitals from a closed‐shell or a half‐electron open‐shell Hartree‐Fock calculation. CPU times for single point energy and gradient calculations are reported. The code allows MRCI geometry optimizations of large molecules, as illustrated for the singlet ground state and the four lowest triplet states of fullerene C76. © 2003 Wiley Periodicals, Inc. J Comput Chem 6: 714–726, 2003

Cai, Yu‐Dong; Liu, Xiao‐Jun; Chou, Kuo‐Chen

doi: 10.1002/jcc.10222pmid: 12666164

The neural network method was applied to the prediction of the content of protein secondary structure elements, including α‐helix, β‐strand, β‐bridge, 310‐helix, π‐helix, H‐bonded turn, bend, and random coil. The “pair‐coupled amino acid composition” originally proposed by K. C. Chou (J Protein Chem 1999, 18, 473) was adopted as the input. Self‐consistency and independent‐dataset tests were used to appraise the performance of the neural network. Results of both tests indicated high performance of the method. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 727–731, 2003

Gill, Peter M. W.; Chien, Siu‐Hung

doi: 10.1002/jcc.10211pmid: 12666165

We introduce a Gaussian quadrature, based on the polynomials that are orthogonal with respect to the weight function ln2x on the interval (0, 1), which is suitable for the evaluation of radial integrals. The quadrature is exact if the non‐Jacobian part of the integrand is a linear combination of a geometric sequence of exponential functions. We find that the new scheme is a useful alternative to existing approaches, particularly for integrands that exhibit multiexponential behavior. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 732–740, 2003

Schulz–Gasch, Tanja; Stahl, Martin

doi: 10.1002/jcc.10147pmid: 12666166

2,3‐Oxidosqualene cyclases (OSC) are key enzymes in sterol biosynthesis. They catalyze the stereoselective cyclization and skeletal rearrangement of (3S)‐2,3‐oxidosqualene to lanosterol in mammals and fungi and to cycloartenol in algae and higher plants. Sequence information and proposed mechanism of 2,3‐oxidosqualene cyclases are closely related to those of squalene‐hopene cyclases (SHC), which represent functional analogs of OSCs in bacteria. SHCs catalyze the cationic cyclization cascade converting the linear triterpene squalene to fused ring compounds called hopanoids. High stereoselectivity and precision of the skeletal rearrangements has aroused the interest of researchers for nearly half a century, and valuable data on studying mechanistic details in the complex enzyme‐catalyzed cyclization cascade has been collected. Today, interest in cyclases is still unbroken, because OSCs became targets for the development of antifungal and hypocholesterolemic drugs. However, due to the large size and membrane‐bound nature of OSCs, three‐dimensional structural information is still not available, thus preventing a complete understanding of the atomic details of the catalytic mechanism. In this work, we discuss results gained from homology modeling of human OSC based on structural information of SHC from Alicyclobacillus acidocaldarius and propose a structural model of human OSC. The model is in accordance with previously performed experimental studies with mechanism‐based suicide inhibitors and mutagenesis experiments with altered activity and product specificity. Structural insight should strongly stimulate structure‐based design of antifungal or cholesterol‐lowering drugs. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 741–753, 2003

Pernpointner, Markus; Visscher, Lucas

doi: 10.1002/jcc.10215pmid: 12666167

Given the importance of the Coupled‐cluster (CC) method as an efficient and accurate way to take electron correlation into account, we extend the parallelization technique in the second part of this series also to the 4‐Spinor CCSD algorithm implemented in the Dirac–Fock packages DIRAC and MOLFDIR. The present implementation is based on the availability of the transformed molecular two‐electron integrals on an external storage medium. The linearity of the CC equations in these two‐electron integrals is used in a parallelization strategy that is based on distribution of the two largest integral classes that carry three or four virtual spinor indices. The corresponding partial contributions to the T1 and T2 amplitudes are calculated on each node and added using Message Passing Interface (MPI) library calls. Although we did not employ a master/slave principle, one specific node was assigned to also perform the remaining serial parts of the algorithm. In the critical sections considerable savings in storage requirements and computer time could be achieved, and this allows for computations on larger systems in the framework of four‐component theory. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 754–759, 2003