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Ab Initio Predictions (ab + initio_prediction)
Selected AbstractsChemInform Abstract: Ab initio Prediction of the Low-Temperature Phase Diagrams in the Systems MBr,MCl (M: Li, Na, K).CHEMINFORM, Issue 37 2008J. C. Schoen Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] ChemInform Abstract: Ab initio Prediction of the Structure and Vibration,Rotation Spectroscopic Properties of Li2OH and Li2OH+.CHEMINFORM, Issue 24 2008Artur Gertych Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Ab initio prediction of optical rotation: Comparison of density functional theory and Hartree-Fock methods for three 2,7,8-trioxabicyclo[3.2.1]octanesCHIRALITY, Issue 4 2002P.J. Stephens Abstract We report ab initio calculations of the frequency-dependent electric dipole-magnetic dipole polarizabilities, ,(,), at the sodium D line frequency and, thence, of the specific rotations, [,]D, of 2,7,8-trioxabicyclo[3.2.1]octane, 1, and its 1-methyl derivative, 2, using the Density Functional Theory (DFT) and Hartree-Fock/Self-Consistent Field (HF/SCF) methodologies. Gauge-invariant (including) atomic orbitals (GIAOs) are used to ensure origin-independent [,]D values. Using large basis sets which include diffuse functions DFT [,]D values are in good agreement with experimental values (175.8° and 139.2° for (1S,5R)- 1 and - 2, respectively); errors are in the range 25,35°. HF/SCF [,]D values, in contrast, are much less accurate; errors are in the range 75,95°. The use of small basis sets which do not include diffuse functions substantially lowers the accuracy of predicted [,]D values, as does the use of the static limit approximation: ,(,) , ,(o). The use of magnetic-field-independent atomic orbitals, FIAOs, instead of GIAOs, leads to origin-dependent, and therefore nonphysical, [,]D values. We also report DFT calculations of [,]D for the 1-phenyl derivative of 1, 3. DFT calculations find two stable conformations, differing in the orientation of the phenyl group, of very similar energy, and separated by low barriers. Values of [,]D predicted using two different algorithms for averaging over phenyl group orientations are in good agreement with experiment. In principle, the absolute configuration (AC) of a chiral molecule can be assigned by comparison of the optical rotation predicted ab initio to the experimental value. Our results demonstrate the critical importance of the choice of ab initio methodology in obtaining reliable optical rotations and, hence, ACs, and show that, at the present time, DFT constitutes the method of choice. Chirality 14:288,296, 2002. © 2002 Wiley-Liss, Inc. [source] Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structurePROTEIN SCIENCE, Issue 12 2004Xiaoduan Ye Abstract Emerging high-throughput techniques for the characterization of protein and protein-complex structures yield noisy data with sparse information content, placing a significant burden on computation to properly interpret the experimental data. One such technique uses cross-linking (chemical or by cysteine oxidation) to confirm or select among proposed structural models (e.g., from fold recognition, ab initio prediction, or docking) by testing the consistency between cross-linking data and model geometry. This paper develops a probabilistic framework for analyzing the information content in cross-linking experiments, accounting for anticipated experimental error. This framework supports a mechanism for planning experiments to optimize the information gained. We evaluate potential experiment plans using explicit trade-offs among key properties of practical importance: discriminability, coverage, balance, ambiguity, and cost. We devise a greedy algorithm that considers those properties and, from a large number of combinatorial possibilities, rapidly selects sets of experiments expected to discriminate pairs of models efficiently. In an application to residue-specific chemical cross-linking, we demonstrate the ability of our approach to plan experiments effectively involving combinations of cross-linkers and introduced mutations. We also describe an experiment plan for the bacteriophage , Tfa chaperone protein in which we plan dicysteine mutants for discriminating threading models by disulfide formation. Preliminary results from a subset of the planned experiments are consistent and demonstrate the practicality of planning. Our methods provide the experimenter with a valuable tool (available from the authors) for understanding and optimizing cross-linking experiments. [source] Soft protein,protein docking in internal coordinatesPROTEIN SCIENCE, Issue 2 2002Juan Fernández-Recio PDB, Protein Data Bank; ICM, Internal Coordinate Mechanics; RMSD, root-mean-square deviation Abstract The association of two biological macromolecules is a fundamental biological phenomenon and an unsolved theoretical problem. Docking methods for ab initio prediction of association of two independently determined protein structures usually fail when they are applied to a large set of complexes, mostly because of inaccuracies in the scoring function and/or difficulties on simulating the rearrangement of the interface residues on binding. In this work we present an efficient pseudo-Brownian rigid-body docking procedure followed by Biased Probability Monte Carlo Minimization of the ligand interacting side-chains. The use of a soft interaction energy function precalculated on a grid, instead of the explicit energy, drastically increased the speed of the procedure. The method was tested on a benchmark of 24 protein,protein complexes in which the three-dimensional structures of their subunits (bound and free) were available. The rank of the near-native conformation in a list of candidate docking solutions was <20 in 85% of complexes with no major backbone motion on binding. Among them, as many as 7 out of 11 (64%) protease-inhibitor complexes can be successfully predicted as the highest rank conformations. The presented method can be further refined to include the binding site predictions and applied to the structures generated by the structural proteomics projects. All scripts are available on the Web. [source] MHC Class II epitope predictive algorithmsIMMUNOLOGY, Issue 3 2010Morten Nielsen Summary Major histocompatibility complex class II (MHC-II) molecules sample peptides from the extracellular space, allowing the immune system to detect the presence of foreign microbes from this compartment. To be able to predict the immune response to given pathogens, a number of methods have been developed to predict peptide,MHC binding. However, few methods other than the pioneering TEPITOPE/ProPred method have been developed for MHC-II. Despite recent progress in method development, the predictive performance for MHC-II remains significantly lower than what can be obtained for MHC-I. One reason for this is that the MHC-II molecule is open at both ends allowing binding of peptides extending out of the groove. The binding core of MHC-II-bound peptides is therefore not known a priori and the binding motif is hence not readily discernible. Recent progress has been obtained by including the flanking residues in the predictions. All attempts to make ab initio predictions based on protein structure have failed to reach predictive performances similar to those that can be obtained by data-driven methods. Thousands of different MHC-II alleles exist in humans. Recently developed pan-specific methods have been able to make reasonably accurate predictions for alleles that were not included in the training data. These methods can be used to define supertypes (clusters) of MHC-II alleles where alleles within each supertype have similar binding specificities. Furthermore, the pan-specific methods have been used to make a graphical atlas such as the MHCMotifviewer, which allows for visual comparison of specificities of different alleles. [source] Absolute configurations of chiral herbicides determined from vibrational circular dichroismCHIRALITY, Issue S1 2005Jiangtao He Abstract Enantiopure herbicides (+)-2-(4-chloro-2-methylphenoxy) propanoic acid, (+)- 1 and (+)-2-(2,4-dichlorophenoxy) propanoic acid, (+)- 2 were investigated using vibrational circular dichroism (VCD). Experimental absorption and VCD spectra of (+)- 1 and (+)- 2 in CDCl3 solution in the 2000,900 cm,1 region were compared with the ab initio predictions of absorption and VCD spectra obtained with density functional theory using the B3LYP/6-31G* basis set for different conformers of (R)- 1 and (R)- 2. Due to the intermolecular hydrogen bonding, this comparison did not provide unambiguous conclusions. To eliminate intermolecular hydrogen bonding influence, the two acids 1 and 2 were converted to the corresponding methyl esters, namely, (+)-methyl 2-(4-chloro-2-methylphenoxy) propanoate, (+)- 3 and (+)-methyl 2-(2,4-dichlorophenoxy) propanoate, (+)- 4. The experimental VCD spectra were measured for these esters and ab initio calculations for different conformers of (R)- 3 and (R)- 4 were carried out. The experimental VCD spectra and corresponding population-weighted theoretical VCD spectra were found to be in excellent agreement, which allowed unambiguous determination of absolute configuration of 3 and 4 as (+)-(R). Since esterification does not invert the configuration, the absolute configuration of the parent acids 1 and 2 is the same as that of corresponding methyl esters. Chirality 17:S1,S8, 2005. © 2004 Wiley-Liss, Inc. [source] Absolute configuration and conformational analysis of a degradation product of inhalation anesthetic Sevoflurane: A vibrational circular dichroism studyCHIRALITY, Issue 8 2002Feng Wang Abstract 1,1,1,3,3-pentafluoro-2-(fluoromethoxy)-3-methoxypropane, compound B, is a product obtained in the degradation of the anesthetic Sevoflurane. Enantiopure (+)- B was investigated using vibrational circular dichroism (VCD). Experimental absorption and VCD spectra of (+)- B in CDCl3 solution in the 2,000,900 cm,1 region are compared with the ab initio predictions of absorption and VCD spectra obtained from density functional theory using B3LYP/6-31G* basis set for different conformers of (S)-1,1,1,3,3-pentafluoro-2-(fluoromethoxy)-3-methoxypropane. This comparison indicates that (+)- B is of the (S)-configuration in CDCl3 solution, in agreement with previous literature results. Our results also indicate that this compound adopts six predominant conformations in CDCl3 solution. Chirality 14:618,624, 2002. © 2002 Wiley-Liss, Inc. [source] | ||||||||||