empirical correlations
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This paper gives two empirical correlations of formation Gibbs energies of gaseous clusters DeltaG(f)n as function of number of solvent molecules attached to the ion, n, and one correlation connecting the DeltaG(f)n for each individual cluster with the total DeltaG(o)hydr value. The experimental ratios of DeltaG(f)2/DeltaG(f)1 and DeltaG(f)3/DeltaG(f)1 for both alkali metal and halide ions are on average equal to 0.75 and 0.5, respectively. DeltaG(f)n values for n > or = 4 are correlated with n as DeltaG(f)n = [a/(n - 1)] DeltaG(f)1 + b DeltaG(f)1. For all available data on cluster energies and each individual cluster, the DeltaG(f)n's are straight-line functions of DeltaG(o)hydr. This well corresponds to another empirical rule stating that the Gibbs energies of transfer of ions between two solvents are often as well straight-line functions of DeltaG(o)(hydr) [J. Rais and T. Okada, J. Phys. Chem. A, 2000, 104, 7314]. Tentative models of the found behavior are proposed. A full data set of the gaseous cluster energies of formation based on inclusion of new, usually not used entries from the literature is provided.
- Publikační typ
- časopisecké články MeSH
- MeSH
- dospělí MeSH
- koronární nemoc psychologie MeSH
- lidé středního věku MeSH
- lidé MeSH
- osobnost typu A * MeSH
- rizikové faktory MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
The currently practiced methods of significance testing in microarray gene expression profiling are highly unstable and tend to be very low in power. These undesirable properties are due to the nature of multiple testing procedures, as well as extremely strong and long-ranged correlations between gene expression levels. In an earlier publication, we identified a special structure in gene expression data that produces a sequence of weakly dependent random variables. This structure, termed the delta-sequence, lies at the heart of a new methodology for selecting differentially expressed genes in nonoverlapping gene pairs. The proposed method has two distinct advantages: (1) it leads to dramatic gains in terms of the mean numbers of true and false discoveries, and in the stability of the results of testing; and (2) its outcomes are entirely free from the log-additive array-specific technical noise. We demonstrate the usefulness of this approach in conjunction with the nonparametric empirical Bayes method. The proposed modification of the empirical Bayes method leads to significant improvements in its performance. The new paradigm arising from the existence of the delta-sequence in biological data offers considerable scope for future developments in this area of methodological research.
Absolute values of (79) geminal (2)J((29) Si-O-(29)Si) couplings were measured in an extensive series of (55) unstrained siloxanes dissolved in chloroform-d. Signs of (2)J((29)Si-O-(29)Si) in some (9) silicon hydrides were determined relative to (1)J((29)Si-(1)H) which are known to be negative. It is supposed that positive sign of the (2)J((29)Si-O-(29)Si) coupling found in all studied hydrides is common to all siloxanes. Theoretical calculations for simple model compounds failed to reproduce this sign and so their predictions of bond length and angle dependences cannot be taken as reliable. Useful empirical correlations were found between the (2)J((29)Si-O-(29)Si) couplings on one side and the total number m of oxygen atoms bonded to the silicon atoms, sum of (29)Si chemical shifts or product of (1)J((29)Si-(13)C) couplings on the other side. The significance of these correlations is briefly discussed.
- Klíčová slova
- 13C NMR, 1J(29Si-13C), 29Si NMR, 29Si chemical shifts, 29Si couplings, 2J(29Si-O-29Si), INADEQUATE, empirical correlations,
- Publikační typ
- časopisecké články MeSH
The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum-chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug-cc-pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled-cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density-functional tight-binding methods covering dispersion energy (DFTB-D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein-inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution.
- MeSH
- chemické modely * MeSH
- cyklin-dependentní kinasa 2 chemie MeSH
- inhibitory proteinkinas chemie MeSH
- konformace proteinů MeSH
- lidé MeSH
- matematické výpočty počítačové * MeSH
- puriny chemie MeSH
- roskovitin MeSH
- sekvence aminokyselin MeSH
- termodynamika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- cyklin-dependentní kinasa 2 MeSH
- inhibitory proteinkinas MeSH
- puriny MeSH
- roskovitin MeSH
An ab initio quantum chemical analysis of the close amino group contacts, existing in many DNA crystal structures, is presented. The calculations are made at the Hartree-Fock (HF) level with medium 6-31G* and 6-31G(NH2*) basis sets as well as with inclusion of correlation energy using the second order Møller-Plesset theory (MP2) with the 6-31G* basis set. We demonstrate that the model system (methylamine dimer, cytosine dimer) amino groups are forced to adopt significantly non-planar geometry to stabilize their mutual interaction. Comparison is made with a representative set of empirical potentials including AMBER, CHARMM and GROMOS. The empirical potentials are not reliable enough to analyze the amino group contacts occurring in the DNA double helices. We propose that the mutual amino group interactions contribute to the conformational variability of the CpG and ApT B-DNA steps.
- MeSH
- chemické jevy MeSH
- cytosin chemie MeSH
- dinukleosidfosfáty chemie MeSH
- DNA chemie MeSH
- fyzikální chemie MeSH
- konformace nukleové kyseliny * MeSH
- methylaminy chemie MeSH
- molekulární sekvence - údaje MeSH
- oligodeoxyribonukleotidy chemie MeSH
- sekvence nukleotidů MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
- Názvy látek
- cytidylyl-3'-5'-guanosine MeSH Prohlížeč
- cytosin MeSH
- dinukleosidfosfáty MeSH
- DNA MeSH
- methylamine MeSH Prohlížeč
- methylaminy MeSH
- oligodeoxyribonukleotidy MeSH
Empirical analyses of experimental data have recently revealed a strong correlation in B- and A-DNA crystal structures between rise of the base pair steps and their cup, or the difference between roll and cup. We show here using empirical potentials that a major part of this correlation can be explained by the base stacking forces. Our calculations further demonstrate that the correlation depends on the base sequence while the dependence is strongest with the C-G step. We also show that small values (which lie beyond resolution of the X-ray diffraction data obtained with the DNA fragment single crystals) of base pair stagger can completely substitute for the effects of roll in the correlation. The present and our previous studies demonstrate that the base pair buckle and stagger can substantially affect base stacking in DNA so that variability of these parameters cannot be neglected in the theoretical analysis of the base sequence effects on DNA conformation.
- MeSH
- difrakce rentgenového záření metody MeSH
- DNA chemie MeSH
- konformace nukleové kyseliny * MeSH
- krystalizace MeSH
- molekulární sekvence - údaje MeSH
- oligodeoxyribonukleotidy MeSH
- sekvence nukleotidů MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
- Názvy látek
- DNA MeSH
- oligodeoxyribonukleotidy MeSH
Interactions between amino acid side chains play a crucial role both within a folded protein and between the interacting protein molecules. Here we have selected a representative set of 24 of the 400 (20 × 20) possible interacting side chain pairs based on data from Atlas of Protein Side-Chain Interactions. For each pair, we obtained its most favorable interaction geometry from the structural data and computed the interaction energy in the gas phase using several different, commonly used, ab initio and force field methods, namely Møller-Plesset perturbation theory (MP2), density functional theory combined with symmetry-adapted perturbation theory (DFT-SAPT), density functional theory empirically augmented with an empirical dispersion term (DFT-D), and empirical potentials using the OPLS-AA/L and Amber03 force fields. All the methods were compared against a reference method taken to be the CCSD(T) level of theory extrapolated to the complete basis set limit. We found a high degree of agreement between the different methods, even though the range of binding energies obtained was extremely large. The most computationally intensive methods yielded the best results. Among the less computationally time-consuming methods, the DFT-D method as well as parm03 force field provided consistently good results when compared to the reference values. We also tested how representative the chosen geometries of the side chains were and investigated the effect on the binding energies of the dielectric constant of the surrounding medium.
- Publikační typ
- časopisecké články MeSH
We compared the results of various microscale indentation creep (microcreep) measurements with macroscale tensile creep (macrocreep) measurements of three common polymers: high-density polyethylene (PE), polypropylene (PP), and polystyrene (PS). The main objective was to verify if the short-term microcreep experiments could predict long-term macrocreep behavior of the selected polymers, whose properties ranged from very soft and ductile (PE) to very hard and brittle (PS). The second objective was to compare several creep predictive schemes: the empirical power law model (PL) and several types of phenomenological elasto-visco-plastic models (EVP). In order to facilitate this task, we developed a universal program package named MCREEP, which fits PL and EVP models to both tensile and indentation creep data. All experimental results and theoretical predictions documented that: (i) regardless of the creep experiment type, both micro- and macrocreep resistance increased in the following order: PE < PP < PS, (ii) the short-term microcreep experiments could be used to predict qualitatively the long-term macrocreep behavior, and (iii) the simple empirical power law model yielded better predictions of long-term creep behavior than the more sophisticated elasto-visco-plastic models.
- Klíčová slova
- indentation creep, microindentation, polymers, tensile creep, viscoelasticity,
- Publikační typ
- časopisecké články MeSH
Neutral (G.GC, A.AT, G.AT, T.AT, and C(imino).GC) and protonated (CH+.GC and AH+.GC) hydrogen-bonded trimers of nucleic acid bases were characterized by ab initio methods with the inclusion of electron correlation. In addition, the influence of metal cations on the third-strand binding in Purine-Purine-Pyrimidine (Pu.PuPy) reverse-Hoogsteen triplets has been studied. The ab initio calculations were compared with those from recently introduced force fields (AMBER4.1, CHARMM23, and CFF95). The three-body term in neutral trimers is mostly negligible, and the use of empirical potentials is justified. The only exception is the neutral G.GC Hoogsteen trimer with a three-body term of -4 kcal/mol. Protonated trimers are stabilized by molecular ion-molecular dipole attraction and the interaction within the complex is nonadditive, with the three-body term on the order of -3 kcal/mol. There is a significant induction interaction between the third-strand protonated base and guanine. The calculations indicate an enhancement of the third-strand binding in the G.GC reverse-Hoogsteen trimer due to-metal cation coordination to the N7/O6 position of the third-strand guanine. Interactions between metal cations and complexes of DNA bases are in general highly non-additive; the three-body term is above-10 kcal/mol in a complex of a divalent cation (Ca2+) with the GG reverse-Hoogsteen pair. The pairwise additive empirical potentials qualitatively underestimate the binding energy between cation and base.
- MeSH
- adenin chemie MeSH
- cytosin chemie MeSH
- DNA chemie MeSH
- guanin chemie MeSH
- kalorimetrie MeSH
- kationty MeSH
- konformace nukleové kyseliny * MeSH
- kovy MeSH
- molekulární modely MeSH
- molekulární struktura MeSH
- počítačová simulace MeSH
- software MeSH
- thymin chemie MeSH
- vodíková vazba MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, P.H.S. MeSH
- Názvy látek
- adenin MeSH
- cytosin MeSH
- DNA MeSH
- guanin MeSH
- kationty MeSH
- kovy MeSH
- thymin MeSH
