Journal of Computational Chemistry

Wang, Jing; Gu, Jiande; Leszczynski, Jerzy

doi: 10.1002/jcc.22991pmid: 22514093

The density functional theory (DFT) with B3LYP, M05‐2x, and M06‐2x functionals, along with the 6‐311+G(d, p) basis set, were used in the study of the UV absorption spectra and the H‐bonding pairing patterns of the sulfur and selenium substituted guanines. The time‐dependent DFT calculations reveal that the red‐shifts of the transition energies predicted for guanine for the first gas‐phase observable transition amount to 55 nm for S6mG and 86 nm for Se6mG, respectively. These changes in the transition energies are qualitatively comparable to the experimental data for substituted guanines in DNA. The density deformation map reveals that both sulfur and selenium atoms exhibit lesser conjugated with the purine ring, which leads to the small transition energies in S6mG and Se6mG. The decrease in binding energy (3 kcal/mol) of Se6mGmC as compared to that of mGmC is well related to the observation of the melting temperature difference ΔTm ∼3.9 °C for the Se‐DNA versus DNA. The molecular recognition (mGmC pairing) pattern is found to be changed significantly due to the replacement of O6 by S or Se. The substantial base–base plane twisting revealed in this study suggests that the base stacking in the DNA might be interrupted. This study shows that the red‐shifts of the transition energies predicted by the M05‐2x and M06‐2x functionals are close to those revealed by the B3LYP calculations. As M05‐2x and M06‐2x offer better descriptions for the dispersion interactions, they provide efficient approaches to investigate the influences of the base‐stacking on the transition energies. © 2012 Wiley Periodicals, Inc.

Buenker, Robert J.; Liebermann, Heinz‐Peter

doi: 10.1002/jcc.22992pmid: 22522712

Ab initio multireference single‐ and double‐excitation configuration interaction calculations have been performed to compute potential curves for ground and excited states of the CaO and SrO molecules and their positronic complexes, e+CaO, and e+SrO. The adiabatic dissociation limit for the 2Σ+ lowest states of the latter systems consists of the positive metal ion ground state (M+) and the OPs complex (e+O−), although the lowest energy limit is thought to be e+M + O. Good agreement is found between the calculated and experimental spectroscopic constants for the neutral diatomics wherever available. The positron affinity of the closed‐shell X 1Σ+ ground states of both systems is found to lie in the 0.16–0.19 eV range, less than half the corresponding values for the lighter members of the alkaline earth monoxide series, BeO and MgO. Annihilation rates (ARs) have been calculated for all four positronated systems for the first time. The variation with bond distance is generally similar to what has been found earlier for the alkali monoxide series of positronic complexes, falling off gradually from the OPs AR value at their respective dissociation limits. The e+SrO system shows some exceptional behavior, however, with its AR value reaching a minimum at a relatively large bond distance and then rising to more than twice the OPs value close to its equilibrium distance. © 2012 Wiley Periodicals, Inc.

Bereźniak, Tomasz; Jäschke, Andres; Smith, Jeremy C.; Imhof, Petra

doi: 10.1002/jcc.22993pmid: 22549366

The Diels‐Alderase ribozyme is an in vitro‐evolved ribonucleic acid enzyme that catalyzes a [4 + 2] cycloaddition reaction between an anthracene diene and a maleimide dienophile. The ribozyme can in principle be used to selectively synthesize only one product enantiomer, depending on which of the two entrances to the catalytic pocket, “front” or “back”, the substrate is permitted to use. Here, we investigate stereoselection and substrate recognition in the ribozyme by means of multiple molecular dynamics simulations, performed on each of the two substrates individually in the pocket, on the reactant state, and on the product state. The results are consistent with a binding mechanism in which the maleimide likely binds first followed by the anthracene, which enters preferentially through the front door. The free energy profiles for anthracene binding indicate that the pre‐(R,R)‐enantiomer conformation is slightly preferred, in agreement with the experimentally observed small enantiomeric excess of the (R,R)‐enantiomer of the product. The reactant state is stabilized by the simultaneous presence of both substrates bound to their binding sites in the hydrophobic pocket as well as by stacking interactions between them. © 2012 Wiley Periodicals, Inc.

Kendrick, John; Leusen, Frank J. J.; Neumann, Marcus A.

doi: 10.1002/jcc.22994pmid: 22528670

Parameters are derived for a molecular mechanics type dispersive correction to solid‐state density functional theory calculations on molecular crystals containing iodine and phosphorous. The molecular C6 coefficients are derived from photoabsorption differential oscillator strength spectra determined from accurate (e,e) dipole spectra. The cross‐over parameters, which ensure correct behavior at short internuclear distances, are obtained by fitting predicted crystal lattice parameters to experimental data. The accuracy of the parameterization is assessed by optimizing the experimental structures of several additional phosphorous and iodine containing molecular crystals and by examining the relative stabilities of the known polymorphs of phosphorous pentoxide and the stabilities of different packings of an iodine containing molecular crystal, 2,9‐bis(iodo)anthanthrone, which has been the subject of a crystal structure prediction study. Optimizations of the experimental crystal structures did not lead to significant geometric deviations. The optimized experimental structure of 2,9‐bis(iodo)anthanthrone is the lowest energy packing found, indicating a satisfactory description of both energy and structure for these molecular crystals. © 2012 Wiley Periodicals, Inc.

Panosetti, Chiara; Hofer, Werner A.

doi: 10.1002/jcc.22998pmid: 22549464

In this work, we have computationally modeled the adsorption of 1,3‐diiodobenzene (meta‐diiodobenzene or m‐DIB) on Cu(1 1 0) by means of density functional theory including van der Waals interaction using Grimme's method. We have compared the adsorption energies and structures of 23 possible configurations of the physisorbed molecule. Furthermore, we have simulated STM images for the four most stable configurations using the Tersoff–Hamann approach at different bias voltages. We find that all the adsorption orientations have comparable energy, and we discuss the relative probabilities of experimental observation. We find that the adsorption induces small distortions in the molecular structure of the adsorbate and in some cases an adsorption‐induced symmetry breakdown occurs. We also find evidence that the most stable arrangement is actually a bistable system with interesting symmetry properties. © 2012 Wiley Periodicals, Inc.

Yesylevskyy, Semen O.

doi: 10.1002/jcc.22989pmid: 22539341

An open‐source Pteros library for molecular modeling and analysis of molecular dynamics trajectories for C++ programming language is introduced. Pteros provides a number of routine analysis operations ranging from reading and writing trajectory files and geometry transformations to structural alignment and computation of nonbonded interaction energies. The library features asynchronous trajectory reading and parallel execution of several analysis routines, which greatly simplifies development of computationally intensive trajectory analysis algorithms. Pteros programming interface is very simple and intuitive while the source code is well documented and easily extendible. Pteros is available for free under open‐source Artistic License from http://sourceforge.net/projects/pteros/. © 2012 Wiley Periodicals, Inc.

Largent, R. Jeffrey; Polik, William F.; Schmidt, J. R.

doi: 10.1002/jcc.22995pmid: 22549414

Symmetry is an extremely useful and powerful tool in computational chemistry, both for predicting the properties of molecules and for simplifying calculations. Although methods for determining the point groups of perfectly symmetric molecules are well‐known, finding the closest point group for a “nearly” symmetric molecule is far less studied, although it presents many useful applications. For this reason, we introduce Symmetrizer, an algorithm designed to determine a molecule's symmetry elements and closest matching point groups based on a user‐adjustable tolerance, and then to symmetrize that molecule to a given point group geometry. In contrast to conventional methods, Symmetrizer takes a bottom‐up approach to symmetry detection by locating all possible symmetry elements and uses this set to deduce the most probable point groups. We explain this approach in detail, and assess the flexibility, robustness, and efficiency of the algorithm with respect to various input parameters on several test molecules. We also demonstrate an application of Symmetrizer by interfacing it with the WebMO web‐based interface to computational chemistry packages as a showcase of its ease of integration. © 2012 Wiley Periodicals, Inc.

Roberts, Benjamin P.; Seabra, Gustavo M.; Roitberg, Adrian E.; Merz, Kenneth M.; Deumens, Erik; Torras, Juan; Trickey, Samuel B.

doi: 10.1002/jcc.23003pmid: 22570199

We comment upon the recent critique of use of the Program for User Package Interfacing and Linking (PUPIL) system for linking AMBER and GAUSSIAN in a multiscale quantum mechanical/molecular mechanics (QM/MM) simulation (Okamoto et al., J. Comput. Chem. 2011, 32, 932). Specifically, their method for computing forces on the MM particles from the QM region via the GAUSSIAN‐03 electrical field was already implemented in PUPIL version 1.3, publicly available beginning December 2009. Some other doubtful characterizations of PUPIL are discussed briefly in the context of current awareness of open‐source codes more generally. © 2012 Wiley Periodicals, Inc.