Journal of Computational Chemistry

Donnini, Serena; Mark, Alan E.; Juffer, André H.; Villa, Alessandra

doi: 10.1002/jcc.20156pmid: 15584080

The incorporation of explicit ions to mimic the effect of ionic strength or to neutralize the overall charge on a system in free energy calculations using molecular dynamics simulations is investigated. The difference in the free energy of hydration between two triosephosphate isomerase inhibitors calculated at five different ion concentrations is used as an example. We show that the free energy difference can be highly sensitive to the presence of explicit ions even in cases where the mutation itself does not involve a change in the overall charge. The effect is most significant if the molecule carries a net charge close to the site mutated. Furthermore, it is shown that the introduction of a small number of ions can lead to very severe sampling problems suggesting that in practical calculations convergence can best be achieved by incorporating either no counterions or by simulating at high ionic strength to ensure sufficient sampling of the ion distribution. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 115–122, 2005

Deeth, Robert J.; Fey, Natalie; Williams–Hubbard, Benjamin

doi: 10.1002/jcc.20137pmid: 15584081

The ligand field molecular mechanics (LFMM) model, which incorporates the ligand field stabilization energy (LFSE) directly into the potential energy expression of molecular mechanics (MM), has been implemented in the “chemically aware” molecular operating environment (MOE) software package. The new program, christened DommiMOE, is derived from our original in‐house code that has been linked to MOE via its applications programming interface and a number of other routines written in MOE's native scientific vector language (SVL). DommiMOE automates the assignment of atom types and their associated parameters and popular force fields available in MOE such as MMFF94, AMBER, and CHARMM can be easily extended to provide a transition metal simulation capability. Some of the unique features of the LFMM are illustrated using MMFF94 and some simple (MCl4)2− and (Ni(NH3)n)2+ species. These studies also demonstrate how density functional theory calculations, especially on experimentally inaccessible systems, provide important data for designing improved LFMM parameters. DommiMOE treats Jahn–Teller distortions automatically, and can compute the relative energies of different spin states for Ni(II) complexes using a single set of LFMM parameters. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 123–130, 2005

De Sancho, David; Prieto, Lidia; Rubio, Ana M.; Rey, Antonio

doi: 10.1002/jcc.20150pmid: 15584079

Genetic algorithms constitute a powerful optimization method that has already been used in the study of the protein folding problem. However, they often suffer from a lack of convergence in a reasonably short time for complex fitness functions. Here, we propose an evolutionary strategy that can reproducibly find structures close to the minimum of a potential function for a simplified protein model in an efficient way. The model reduces the number of degrees of freedom of the system by treating the protein structure as composed of rigid fragments. The search incorporates a double encoding procedure and a merging operation from subpopulations that evolve independently of one another, both contributing to the good performance of the full algorithm. We have tested it with protein structures of different degrees of complexity, and present our conclusions related to its possible application as an efficient tool for the analysis of folding potentials. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 131–141, 2005

Depizzol, Daniela Bertolini; Paiva, Marcia Helena Moreira; Dos Santos, Thiago Oliveira; Gaudio, Anderson Coser

doi: 10.1002/jcc.20151pmid: 15584073

A new computer program called MoCalc (Molecular Calculations) has been designed to help the computational chemistry practitioner in the task of performing and analyzing molecular calculations. MoCalc is a graphical user interface for the MO calculation programs Gamess and Mopac, and uses Rasmol and Babel for molecule display and file conversion, respectively. In its initial version, MoCalc can execute the following operations: (a) create and handle Gamess and Mopac input files; (b) import any kind of molecular geometry supported by Babel and paste it as Cartesian, internal, or Gaussian‐type coordinates on the input file; (c) convert Gamess and Mopac output files to inputs of both programs; (d) edit and validate the keywords that control the Gamess and Mopac calculation procedure; (e) display the input (Mopac) and output (Gamess and Mopac) molecular geometries; (f) run single or multiple (batch) calculations, either interactively or in background; (g) automatically open the output files as soon as the calculation finishes; (h) extract results from the output files, such as energy, charges, dipole, population analysis, wave function, bond orders, and valence analysis, and display them in spreadsheets; (i) calculate reactivity indices derived from the frontier orbital theory and the root‐mean‐square (rms) deviation of input and output geometries. All the results generated by MoCalc can be promptly transferred to text editors and electronic spreadsheets, which facilitate a detailed subsequent analysis and the publication of the results. MoCalc can also perform graphical and numerical comparative analysis of the some results when more than one output file is loaded. The program was coded in Visual Basic and runs in Windows 95/98/NT4/ME/2000/XP environments. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 142–144, 2005

Benkova, Zuzana; Sadlej, Andrzej J.; Oakes, Roma E.; Bell, Steven E. J.

doi: 10.1002/jcc.20149pmid: 15584074

Following the recent studies of basis sets explicitly dependent on oscillatory external electric field we have investigated the possibility of some further truncation of the so‐called polarized basis sets without any major deterioration of the computed data for molecular dipole moments, dipole polarizabilities, and related electric properties of molecules. It has been found that basis sets of contracted Gaussian functions of the form (3s1p) for H and (4s3p1d) for the first‐row atoms can satisfy this requirement with particular choice of contractions in their polarization part. With m denoting the number of primitive GTOs in the contracted polarization function, the basis sets devised in this article will be referred to as the ZmPol sets. In comparison with earlier, medium‐size polarized basis sets (PolX), these new ZmPol basis sets are reduced by 2/3 in their size and lead to the order of magnitude computing time savings for large molecules. Simultaneously, the dipole moment and polarizability data remain at almost the same level of accuracy as in the case of the PolX sets. Among a variety of possible applications in computational chemistry, the ZmPolX are also to be used for calculations of frequencies and intensities in the Raman spectra of large organic molecules (see Part II, this issue). © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 145–153, 2005

Oakes, Roma E.; Bell, Steven E. J.; Benkova, Zuzana; Sadlej, Andrzej J.

doi: 10.1002/jcc.20158pmid: 15584075

The accuracies of the calculated vibrational frequencies and Raman intensities given by two new, highly compact Pol‐type basis sets, Z2PolX and Z3PolX, have been determined and compared to the 6‐31G(d), PolX, and aug‐cc‐pVTZ basis sets. Calculation of accurate Raman intensities has previously required large basis sets, but the ZmPolX basis sets are smaller even than PolX, which are the most compact basis sets able to calculate accurate Raman intensities. For the largest compound studied, C5H10O2, Z3PolX required more than an order of magnitude less CPU time than PolX, which has been shown to be 10 times faster than aug‐cc‐pVTZ. Two sets of test molecules were studied: one was a series of small molecules for which experimental values for absolute Raman activities were available; the second was a series of medium‐sized molecules (mainly common organic solvents) where only relative Raman band intensities were available. The accuracies of the Raman intensities given by both of the ZmPolX basis sets were good compared to those of the PolX and aug‐cc‐pVTZ sets, and much better than the 6‐31G(d) values. The errors in even unscaled frequency values <2000 cm−1 were also acceptable and were slightly lower for Z3PolX than Z2PolX (30 cm−1 vs. 48 cm−1). The combination of good intensity and frequency data meant that for the medium‐sized organic molecules there was a close correspondence between the simulated Raman spectra and experimental data, and that the observed bands could easily be assigned on the basis of these calculations. Achieving this level of accuracy in the simulations at modest computational cost should now allow computational methods to be combined with experimental Raman studies much more widely than is currently the case. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 154–159, 2005

Wada, Mitsuhito; Sakurai, Minoru

doi: 10.1002/jcc.20154pmid: 15586398

A quantum chemical method for rapid optimization of protein structures is proposed. In this method, a protein structure is treated as an assembly of amino acid units, and the geometry optimization of each unit is performed with taking the effect of its surrounding environment into account. The optimized geometry of a whole protein is obtained by repeated application of such a local optimization procedure over the entire part of the protein. Here, we implemented this method in the MOPAC program and performed geometry optimization for three different sizes of proteins. Consequently, these results demonstrate that the total energies of the proteins are much efficiently minimized compared with the use of conventional optimization methods, including the MOZYME algorithm (a representative linear‐scaling method) with the BFGS routine. The proposed method is superior to the conventional methods in both CPU time and memory requirements. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 160–168, 2005

Sun, H.; Kung, P. W.‐C.

doi: 10.1002/jcc.20153pmid: 15586399

We have studied the gaseous and solid phases of urea using both quantum mechanics calculation and force field simulation methods. Our ab initio calculations confirmed experimental observations that urea structure is planar in the crystal, but nonplanar in the gas phase. Based on electron structure analysis, we suggest that the significant difference between these two structures in different environments can be qualitatively explained by two resonance structures. The planar structure is more polarized than the nonplanar one, and the former is stabilized in the solid phases due to strong electrostatic interactions. We found classical force field method is incapable to represent such strong polarization effect. Using molecular dynamics simulations with a force field optimized for condensed phases, we calculated the crystalline structures of urea in the temperature range of 12 to 293 K. The densities as well as cell parameters are within 2% deviation from the experimental data in the temperature range. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 169–174, 2005

Chiodo, S.; Russo, N.; Sicilia, E.

doi: 10.1002/jcc.20144pmid: 15586396

Optimized contracted Gaussian basis sets of double‐zeta valence polarized (DZVP) quality for first‐row transition metals are presented. The DZVP functions were optimized using the PWP86 generalized gradient approximation (GGA) functional and the B3LYP hybrid functional. For a careful analysis of the basis sets performance the transition metal atoms and cations excitation energies were calculated and compared with the experimental ones. The calculated values were also compared with those obtained using the previously available DZVP basis sets developed at the local‐density functional level. Because the new basis sets work better than the previous ones, possible reasons of this behavior are analyzed. The newly developed basis sets also provide a good estimation of other atomic properties such as ionization energies. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 175–183, 2005

Wang, Li; Liu, Jing‐Yao; Li, Ze‐Sheng; Sun, Chia‐Chung

doi: 10.1002/jcc.20159pmid: 15593347

The mechanisms of the SH (SD) radicals with Cl2 (R1), Br2 (R2), and BrCl (R3) are investigated theoretically, and the rate constants are calculated using a dual‐level direct dynamics method. The optimized geometries and frequencies of the stationary points are calculated at the MP2/6‐311G(d,p) and MPW1K/6‐311G(d,p) levels. Higher‐level energies are obtained at the approximate QCISD(T)/6‐311++G(3df, 2pd) level using the MP2 geometries as well as by the multicoefficient correlation method based on QCISD (MC‐QCISD) using the MPW1K geometries. Complexes with energies less than those of the reactants or products are located at the entrance or the exit channels of these reactions, which indicate that the reactions may proceed via an indirect mechanism. The enthalpies of formation for the species XSH/XSD (X = Cl and Br) are evaluated using hydrogenation working reactions method. By canonical variational transition‐state theory (CVT), the rate constants of SH and SD radicals with Cl2, Br2, and BrCl are calculated over a wide temperature range of 200–2000 K at the a‐QCISD(T)/6‐311++G(3df, 2pd)//MP2/6‐311G(d, p) level. Good agreement between the calculated and experimental rate constants is obtained in the measured temperature range. Our calculations show that for SH (SD) + BrCl reaction bromine abstraction (R3a or R3a′) leading to the formation of BrSH (BrSD) + Cl in a barrierless process dominants the reaction with the branching ratios for channels 3a and 3a′ of 99% at 298 K, which is quite different from the experimental result of k3a′/k3′ = 54 ± 10%. Negative activation energies are found at the higher level for the SH + Br2 and SH + BrCl (Br‐abstraction) reactions; as a result, the rate constants show a slightly negative temperature dependence, which is consistent with the determination in the literature. The kinetic isotope effects for the three reactions are “inverse”. The values of kH/kD are 0.88, 0.91, and 0.69 at room temperature, respectively, and they increase as the temperature increases. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 184–193, 2005