COBRAMM 2.0 — A software interface for tailoring molecular electronic structure calculations and running nanoscale (QM/MM) simulations

We present a new version of the simulation software COBRAMM, a program package interfacing widely known commercial and academic software for molecular modeling. It allows a problem-driven tailoring of computational chemistry simulations with effortless ground and excited-state electronic structure computations. Calculations can be executed within a pure QM or combined quantum mechanical/molecular mechanical (QM/MM) framework, bridging from the atomistic to the nanoscale. The user can perform all necessary steps to simulate ground state and photoreactions in vacuum, complex biopolymer, or solvent environments. Starting from ground-state optimization, reaction path computations, initial conditions sampling, spectroscopy simulation, and photodynamics with deactivation events, COBRAMM is designed to assist in characterization and analysis of complex molecular materials and their properties. Interpretation of recorded spectra range from steady-state to time-resolved measurements. Various tools help the user to set up the system of interest and analyze the results.     

The coordination chemistry of the structural zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations

The coordination chemistry of the structural zinc ion in horse liver alcohol dehydrogenase has been examined by quantum chemical geometry optimisations. It is shown that all four cysteine ligands are deprotonated in the enzyme, not only two of them as has been suggested. The Zn-S bond lengths are very sensitive to the theoretical treatment; in vacuum they are predicted to be 15 pm longer than in the crystal structure. Half of this discrepancy is due to electronic correlation, the rest can be attributed to screening of the negative sulphide charges by the enzyme, in particular by N-H-S hydrogen bonds. The potential surface is rather flat, so the large difference in geometry between the crystal and the vacuum structure corresponds to an energy change of less than 35 kJ/mol. The experimental bond lengths can be reproduced only with methods that account explicitly for the enzyme. A dielectric continuum model gives bond lengths which are too long, indicating that the enzyme solvates the coordination sphere better than water. Thus, the structural zinc ion can be used as a sensitive test of methods which try to model the surrounding medium in quantum chemical computations.     

From computational quantum chemistry to computational biology: experiments and computations are (full) partners

Computations are being integrated into biological research at an increasingly fast pace. This has not only changed the way in which biological information is managed; it has also changed the way in which experiments are planned in order to obtain information from nature. Can experiments and computations be full partners? Computational chemistry has expanded over the years, proceeding from computations of a hydrogen molecule toward the challenging goal of systems biology, which attempts to handle the entire living cell. Applying theories from ab initio quantum mechanics to simplified models, the virtual worlds explored by computations provide replicas of real-world phenomena. At the same time, the virtual worlds can affect our perception of the real world. Computational biology targets a world of complex organization, for which a unified theory is unlikely to exist. A computational biology model, even if it has a clear physical or chemical basis, may not reduce to physics and chemistry. At the molecular level, computational biology and experimental biology have already been partners, mutually benefiting from each other. For the perception to become reality, computation and experiment should be united as full partners in biological research.     

Molecular properties of a bent-core nematic liquid crystal A131 by multi-level theory simulations

ABSTRACT

Multi-level theory simulations have been performed to model a number of important molecular properties of a bent-core nematic liquid crystal (LC) A131. These important properties include molecular conformations, molecular Raman spectra, differential polarisability ratios, molecular crystals packing, atomic LC structures, order parameters, and Raman depolarisation spectra. The simulations contain four theory levels, involving molecular quantum chemistry, molecular crystal packing, super cell density functional based tight binding optimisation, and super cell molecular dynamics calculations. To heat initial optimised super cell structures, molecular dynamics simulations reveal phase transitions to uniaxial and biaxial nematic phases from molecular crystals. LC atomic structures result in direct calculations on order parameters, which can be further applied to computations on Raman depolarisation spectra with differential polarisability ratios, obtained in the molecular quantum chemistry theory level. The good agreement of simulated Raman depolarisation spectra with the experiment provides a detailed analysis on the unusually low values of experimental uniaxial order parameters.     

Accurate geometries for “Mountain pass” regions of the Ramachandran plot using quantum chemical calculations

Unusual local arrangements of protein in Ramachandran space are not well represented by standard geometry tools used in either protein structure refinement using simple harmonic geometry restraints or in protein simulations using molecular mechanics force fields. In contrast, quantum chemical computations using small poly‐peptide molecular models can predict accurate geometries for any well‐defined backbone Ramachandran orientation. For conformations along transition regions—ϕ from −60 to 60°—a very good agreement with representative high‐resolution experimental X‐ray (≤1.5 Å) protein structures is obtained for both backbone C⁻¹‐N‐C_α angle and the nonbonded O⁻¹…C distance, while “standard geometry” leads to the “clashing” of O…C atoms and Amber FF99SB predicts distances too large by about 0.15 Å. These results confirm that quantum chemistry computations add valuable support for detailed analysis of local structural arrangements in proteins, providing improved or missing data for less understood high‐energy or unusual regions.     

GEOCHEM-EZ: a chemical speciation program with greater power and flexibility

GEOCHEM-EZ is a multi-functional chemical speciation program, designed to replace GEOCHEM-PC, which can only be used on DOS consoles. Chemical speciation programs, such as GEOCHEM and GEOCHEM-PC, have been excellent tools for scientists designing appropriate solutions for their experiments. GEOCHEM-PC is widely used in plant nutrition and soil and environmental chemistry research to perform equilibrium speciation computations, allowing the user to estimate solution ion activities and to consider simple complexes and solid phases. As helpful as GEOCHEM-PC has been to scientists, the consensus was that the program was not very user friendly, was difficult to learn and to troubleshoot, and suffered from several functional weaknesses. To enhance the usability and to address the problems found in GEOCHEM-PC, we upgraded the program with a Java graphical interface, added Help files, and improved its power and function, allowing it to run on any computer that supports Windows XP, Vista or Windows 7.     

A theoretical study on the optical absorption of green fluorescent protein chromophore in solutions

Ethyl 4-(4-hydroxyphenyl) methylidene- 2-methyl-5-oxoimidazolacetate (HBMIA) is a model chromophore of green fluorescent protein. The electronic structure of HBMIA in aqueous solution phase is studied using a hybrid method of quantum chemistry and statistical mechanics, RISM-SCF-SEDD. The solvatochromic shift is correctly reproduced by the present computations.     

ProteoWizard: open source software for rapid proteomics tools development

SUMMARY: The ProteoWizard software project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations. The library contains readers and writers of the mzML data format, which has been written using modern C++ techniques and design principles and supports a variety of platforms with native compilers. The software has been specifically released under the Apache v2 license to ensure it can be used in both academic and commercial projects. In addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the ProteoWizard library. AVAILABILITY: Cross-platform software that compiles using native compilers (i.e. GCC on Linux, MSVC on Windows and XCode on OSX) is available for download free of charge, at http://proteowizard.sourceforge.net. This website also provides code examples, and documentation. It is our hope the ProteoWizard project will become a standard platform for proteomics development; consequently, code use, contribution and further development are strongly encouraged.