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Application of variational reduced-density-matrix theory to the potential energy surfaces of the nitrogen and carbon dimers.

The acceleration of the variational two-electron reduced-density-matrix (2-RDM) method, using a new first-order algorithm [D. A. Mazziotti, Phys. Rev. Lett. 93, 213001 (2004)], has shown its usefulness in the accurate description of potential energy surfaces in nontrivial basis sets. Here we apply the first-order 2-RDM method to the potential energy surfaces of the nitrogen and carbon dimers in polarized valence double-zeta basis sets for which benchmark full-configuration-interaction calculations exist. In a wave function formalism accurately stretching the triple bond of the nitrogen dimer requires at least six-particle excitations from the Hartree-Fock reference. Furthermore, cleaving the double bond of C2 should produce a "non-Morse"-like potential curve because the ground state near equilibrium (X 1sigma(g)+) has an avoided crossing with the second excited state (B' 1sigma(g)+) and a level crossing with the first excited state (B 1delta(g)). Because the 2-RDM method variationally optimizes the energy over correlated 2-RDMs on the two-electron space without parametrization of the many-electron wave function, it captures multireference correlations that are difficult to describe with approximate wave functions. The 2-RDM method yields for N2 a potential energy surface with features and spectroscopic constants that are more accurate than those from single-reference methods and similar in accuracy to multireference techniques, and it describes the non-Morse-like behavior of C2 which is not captured by single-reference methods.

Journal Article↗

First-principles calculation of geometry and anharmonic vibrational spectra of thioformamide and thioformamide-d2.

The equilibrium geometry of thioformamide HCSNH2 has been determined at the MP2 and CCSD(T) electron correlation levels under C(s) symmetry constraints using triple-zeta basis sets up to cc-pVTZ. All optimized planar structures are true minima on the potential-energy surface and are characterized by the C-N bond length within 1.353-1.343 A, C-S distances of 1.656-1.628 A, and NCS angle between 125.7 degrees and 125.9 degrees . The wave number of the NH2 out-of-plane wagging mode computed in the harmonic approximation shows stronger dependence on the basis set rather than the electron correlation level and varies from 85.9 cm(-1) at CCSD(T)cc-pVDZ level to 335 cm(-1) at MP2/aug-cc-pVTZ level. Anharmonic vibrational spectra of HCSNH2 and HCSND2 have been determined directly from the potential-energy surfaces computed at MP2 level in triple-zeta valence (TZV)(2df,2p) and TZV+(2df,2p) basis sets using vibrational self-consistent-field (VSCF) and correlation-corrected VSCF (CC-VSCF) methods. CC-VSCF wave numbers of fundamental, first overtone, and most intense combination transitions are reported for thioformamide and those of fundamentals for thioformamide-d2. The NH2 wagging (nu12) mode is strongly anharmonic and its fundamentals have been computed at 406.9 cm(-1) [TZV(2df,2p)] and 399.5 cm(-1) [TZV+(2df,2p)], which is remarkably close to the experimental energy of 393 cm(-1). Anharmonically computed fundamentals of this mode in thioformamide-d2, 299.7 cm(-1) [TZV(2df,2p)] and 299.6 cm(-1) [TZV+(2df,2p)], are only approximately 7 cm(-1) higher than the transition energy (293 cm(-1)) observed in the gas phase spectrum of HCSND2. The first overtone of the NH2 wagging mode of thioformamide (nu12 (02)) has been calculated by CC-VSCF procedure at 830.8 cm(-1) [TZV(2df,2p)] and 880.0 cm(-1) [TZV+(2df,2p)], which implies "negative" (nu12 (02)>2*nu12 (01)) anharmonicity of this mode.

Journal Article↗

Electromechanical response of articular cartilage in indentation--considerations on the determination of cartilage properties during arthroscopy.

A finite element formulation of streaming potentials in articular cartilage was incorporated into a fibril-reinforced model using the commercial software ABAQUS. This model was subsequently used to simulate interactions between an arthroscopic probe and articular cartilage in a knee joint. Fibril reinforcement was found to account for large fluid pressure at considerable strain rates, as has been observed in un-confined compression. Furthermore, specific electromechanical responses were associated with specific changes in tissue properties that occur with cartilage degeneration. For example, the strong strain-rate dependence of the load response was only observed when the collagen network was intact. Therefore, it is possible to use data measured during arthroscopy to evaluate the degree of cartilage degeneration and the source causing changed properties. However, practical problems, such as the difficulty of controlling the speed of the hand-held probe, may greatly reduce the reliability of such evaluations. The fibril-reinforced electromechanical model revealed that high-speed transient responses were associated with the collagen network, and equilibrium response was primarily determined by proteoglycan matrix. The results presented here may be useful in the application of arthroscopic tools for evaluating cartilage degeneration, for the proper interpretation of data, and for the optimization of data collection during arthroscopy.

Animals↗

Synthesis and spectroscopic characterization of site-specific 2-amino-1-methyl-6-phenylimidazo.

The aim of the present study is to determine the chemical structure and conformation of DNA adducts formed by incubation of the bioactive form of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), N-acetoxy-PhIP, with a single-stranded 11mer oligodeoxyribonucleotide. Using conditions optimized to give the C8-dG-PhIP adduct as the major product, sufficient material was synthesized for NMR solution structure determination. The NMR data indicate that in duplex DNA this adduct exists in equilibrium between two different conformational states. In the main conformer, the covalently bound PhIP molecule intercalates in the helix, whilst in the minor conformation the PhIP ligand is probably solvent exposed. In addition to the C8-dG-PhIP adduct, at least eight polar adducts are found after reaction of N-acetoxy-PhIP with the oligonucleotide. Three of these were purified for further characterization and shown to exhibit lowest energy UV absorption bands in the range 342-347 nm, confirming the presence of PhIP or PhIP derivative. Accurate mass determination of two of the polar adducts by negative ion MALDI-TOF MS revealed ions consistent with a spirobisguanidino-PhIP derivative and a ring-opened adduct. The third adduct, which has the same mass as the C8-dG-PhIP oligonucleotide adduct, may contain PhIP bound to the N2 position of guanine.

Base Sequence↗

On the regulatory significance of inhibitors acting on non-equilibrium enzymes in the Calvin photosynthesis cycle.

Control analyses and kinetic model studies have been performed in order to obtain quantitative information on the regulatory significance of 12 experimentally well-documented inhibitory interactions of Calvin cycle intermediates with the four non-equilibrium cycle enzymes. Evidence is presented to show that none of these interactions contributes significantly to the cycle flux control over the range of external orthophosphate concentrations where the reaction cycle shows close to optimal activity. Contrary to what has been generally supposed, the examined inhibitions appear to be of little interest for our understanding of the biological regulation of the Calvin photosynthesis cycle under conditions of light and carbon dioxide saturation.

Carbon Dioxide↗

B lymphocyte-induced maturation protein (Blimp)-1, IFN regulatory factor (IRF)-1, and IRF-2 can bind to the same regulatory sites.

The transcriptional repressor B lymphocyte-induced maturation protein-1 (Blimp-1) is expressed in some differentiated cells and is required for terminal differentiation of B cells. To facilitate identification of Blimp-1 target genes, we have determined the optimal DNA recognition sequence for Blimp-1. The consensus is very similar to a subset of sites recognized by IFN regulatory factors (IRFs) that contain the sequence GAAAG. By binding competition and determination of equilibrium dissociation constants, we show that Blimp-1, IRF-1, and IRF-2 have similar binding affinities for functionally important regulatory sites containing this sequence. However, Blimp-1 does not bind to all IRF sites, and specifically does not recognize IRF-4/PU.1 or IRF-8 sites lacking the GAAAG sequence. Chromatin immunoprecipitation studies showed that Blimp-1, IRF-1, and IRF-2 all bind the IFN-beta promoter in vivo, as predicted by the in vitro binding parameters, and in cotransfections Blimp-1 inhibits IRF-1-dependent activation of the IFN-beta promoter. Thus, our data suggest that Blimp-1 competes in vivo with a subset of IRF proteins and help predict the sites and IRF family members that may be affected.

Animals↗

Physical and kinetic properties of a pyridoxal reductase purified from bakers' yeast.

Pyridoxine dehydrogenase (1.1.1.65) (pyridoxal reductase), purified to homogeneity from baker's yeast, is a monomer of Mr approximately 33,000. It catalyzes the reversible oxidation of pyridoxine by NADP to yield pyridoxal and NADPH; equilibrium lies far in the direction of pyridoxine formation (Keq approximately 1.4 X 10(11) l/mol at 25 degrees C). Reduction of pyridoxal occurs most rapidly at pH 6.0-7.0; oxidation of pyridoxine is optimal at pH 8.6. NAD and NADH do not replace NADP and NADPH as substrates; pyridoxine, pyridoxal and pyridoxal 5'-phosphate are the only naturally occurring cosubstrates found. Several other aromatic aldehydes also are reduced, but substrate specificity and other properties of the enzyme distinguish it clearly from other alcohol dehydrogenases or aldehyde reductases. Between pH 6.3 and 7.1 (the intracellular pH of yeast), V/Km with pyridoxal and NADPH as substrates is greater than 600 times that observed with pyridoxine and NADPH as substrates is greater than 600 times that observed with pyridoxine and NADP as substrates. These and other considerations strongly indicate that the dehydrogenase functions in vivo to reduce pyridoxal to pyridoxine, which is the preferred substrate for pyridoxal (pyridoxine) kinase in yeast.

Alcohol Oxidoreductases↗

Estimation of the net acid load of the diet of ancestral preagricultural Homo sapiens and their hominid ancestors.

BACKGROUND: Natural selection has had < 1% of hominid evolutionary time to eliminate the inevitable maladaptations consequent to the profound transformation of the human diet resulting from the inventions of agriculture and animal husbandry. OBJECTIVE: The objective was to estimate the net systemic load of acid (net endogenous acid production; NEAP) from retrojected ancestral preagricultural diets and to compare it with that of contemporary diets, which are characterized by an imbalance of nutrient precursors of hydrogen and bicarbonate ions that induces a lifelong, low-grade, pathogenically significant systemic metabolic acidosis. DESIGN: Using established computational methods, we computed NEAP for a large number of retrojected ancestral preagricultural diets and compared them with computed and measured values for typical American diets. RESULTS: The mean (+/- SD) NEAP for 159 retrojected preagricultural diets was -88 +/- 82 mEq/d; 87% were net base-producing. The computational model predicted NEAP for the average American diet (as recorded in the third National Health and Nutrition Examination Survey) as 48 mEq/d, within a few percentage points of published measured values for free-living Americans; the model, therefore, was not biased toward generating negative NEAP values. The historical shift from negative to positive NEAP was accounted for by the displacement of high-bicarbonate-yielding plant foods in the ancestral diet by cereal grains and energy-dense, nutrient-poor foods in the contemporary diet-neither of which are net base-producing. CONCLUSIONS: The findings suggest that diet-induced metabolic acidosis and its sequelae in humans eating contemporary diets reflect a mismatch between the nutrient composition of the diet and genetically determined nutritional requirements for optimal systemic acid-base status.

Acid-Base Equilibrium↗

A practical approach to the balance between acid production and renal acid excretion in humans.

Precise measurements of net endogenous acid production (NEAP) to determine net acid balance require labor and laboratory intensive steady-state measurements of dietary nutrient intakes and urine and stool composition. In an effort to simplify the task, investigators have devised several alternative methodologies, especially computational predictive models based on diet composition. This paper describes the so-called gold standard, and the details of each alternative methodology, discussing their strengths and potential pitfalls. We also briefly discuss what we believe the optimal NEAP for adult humans, and how to achieve that through diet.

Acid-Base Equilibrium↗

Rate and equilibrium constant of the reaction of 1-methylvinoxy radicals with O2: CH3COCH2 + O2<--> CH3COCH2O2.

The reaction of 1-methylvinoxy radicals, CH3COCH2, with molecular oxygen has been investigated by experimental and theoretical methods as a function of temperature (291-520 K) and pressure (0.042-10 bar He). Experiments have been performed by laser photolysis coupled to a detection of 1-methylvinoxy radicals by laser-induced fluorescence LIF. The potential energy surface calculations were performed using ab inito molecular orbital theory at the G3MP2B3 and CBSQB3 level of theory based on the density function theory optimized geometries. Derived molecular properties of the characteristic points of the potential energy surface were used to describe the mechanism and kinetics of the reaction under investigation. At 295 K, no pressure dependence of the rate constant for the association reaction has been observed: k(1,298K) = (1.18 +/- 0.04) x 10(-12) cm3 s(-1). Biexponential decays have been observed in the temperature range 459-520 K and have been interpreted as an equilibrium reaction. The temperature-dependent equilibrium constants have been extracted from these decays and a standard reaction enthalpy of deltaH(r,298K) = -105.0 +/- 2.0 kJ mol(-1) and entropy of deltaS(r,298K) = -143.0 +/- 4.0 J mol(-1) K(-1) were derived, in excellent agreement with the theoretical results. Consistent heats of formation for the vinoxy and the 1-methylvinoxy radical as well as their O2 adducts are recommended based on our complementary experimental and theoretical study deltaH(f,298K) = 13.0 +/- 2.0, -32. 9+/- 2.0, -85.9 +/- 4.0, and -142.1 +/- 4.0 kJ mol(-1) for CH2CHO, CH3COCH2 radicals, and their adducts, respectively.

Journal Article↗

Injury and protection in split-thickness skin after very rapid cooling and warming.

The ability of low glycerol concentrations and high cooling and warming rates to optimize the survival of frozen/thawed split-thickness porcine skin was investigated. 1H nuclear magnetic resonance spectroscopy was used to measure the diffusion kinetics of glycerol in skin at 4, 12, and 22 degrees C. Equilibrium concentrations were 44 to 69% of the external bathing medium. Rate constants for glycerol diffusion (D/l2) were calculated from the uptake data using a plane sheet model and a least squares method and were independent of external glycerol concentrations: D/l2 = 3.84 x 10(-4) 8-1 at 4 degrees C with an activation energy of 11.2 +/- 4.3 kcal/mol. Skin was cooled rapidly (-5100 degrees C/min) after different times of glycerol permeation at 4 or 22 degrees C, and survival was assessed after warming (+5400 degrees C/min) by an oxygen consumption assay. Recovery of aerobic activity increased in a concentration-dependent manner, and reached 100% after a 10-min exposure to 2 M glycerol at 4 degrees C or 3 min at 22 degrees C, for an uptake of 1.1 M glycerol. Light micrographs of freeze-substituted skin showed a glycerol-dependent decrease in the nucleation and growth of ice in the dermis and epidermis after rapid cooling. A 5-mm exposure to 2 M glycerol at 22 degrees C resulted in the elimination of all observable epidermal ice, except for extremely small ice crystals (< or = 0.5 micron diameter) in the intercellular spaces and in few nuclei, and complete preservation of the fibrous structure of dermal collagen bundles. This cryoprotective mechanism has the potential to offer complete protection of both dermal and viable epidermal targets of freeze/thaw injury and may be applicable to other thin, membranous tissues.

Animals↗

A hydroxylapatite microassay for receptor binding of 2,3,7,8-tetrachlorodibenzo-p-dioxin and 3-methylcholanthrene in various target tissues.

A "batch" hydroxylapatite assay for the 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) receptor that does not require detergents is described. The receptor could be assayed in rat target tissues using either of the cytochrome P1-450 inducers [3H]TCDD or [3H]3-methylcholanthrene as radioligands. A phosphate buffer washing procedure was developed on the basis of chromatographic data and optimized to separate nonspecifically and specifically bound ligand. The assay was characterized with respect to washing efficiency, binding specificity, competition, adsorption time, amount of hydroxylapatite required to bind receptor complexes, sensitivity, and effects of detergents. Equilibrium binding parameters were determined. Receptor extracted with phosphate from hydroxylapatite was analyzed on sucrose gradients and was found to exhibit the same sedimentation properties as the receptor in crude cytosol. Furthermore, the applicability of the assay has been demonstrated in cytosolic preparations from three different target tissues: liver, lung, and thymus.

Animals↗

Absolute exponential stability of recurrent neural networks with Lipschitz-continuous activation functions and time delays.

This paper investigates the absolute exponential stability of a general class of delayed neural networks, which require the activation functions to be partially Lipschitz continuous and monotone nondecreasing only, but not necessarily differentiable or bounded. Three new sufficient conditions are derived to ascertain whether or not the equilibrium points of the delayed neural networks with additively diagonally stable interconnection matrices are absolutely exponentially stable by using delay Halanay-type inequality and Lyapunov function. The stability criteria are also suitable for delayed optimization neural networks and delayed cellular neural networks whose activation functions are often nondifferentiable or unbounded. The results herein answer a question: if a neural network without any delay is absolutely exponentially stable, then under what additional conditions, the neural networks with delay is also absolutely exponentially stable.

Algorithms↗

Optimizing the structures of minimum and transition state on the free energy surface.

Presented here is the application of a scheme for optimizing the structures of minima and transition states on the free energy surface (FES) for a path along a fixed reaction coordinate with the aid of ab initio molecular dynamics (AIMD) simulation. In the direction of the reaction coordinate, the values corresponding to the stationary points were optimized using the quasi-Newton method, in which the gradient of the free energy along the reaction coordinate was obtained by a constraint AIMD method, and the Bofill Hessian update scheme was used. The equilibrium values for the other directions were taken as the corresponding averages in the dynamic simulation. This scheme was applied to several elementary bimolecular addition reactions: (A) BH(3) + H(2)O --> H(2)O.BH(3); (B) BF(3) + NH(3) --> FB(3).NH(3); (C) SO(3) + NH(3) --> O(3)S.NH(3); (D) C(2)H(4) + CCl(2) --> H(4)C(2).CCl(2); (E) Ni(NH(2))(2) + PH(3) --> (NH(2))(2)Ni.PH(3); (F) W(CO)(5) + CO --> W(CO)(6). For reactions A, B, C, and F, no transition state (TS) exists on the potential energy surface (PES). However there is a TS on the FES. This stems from the curvature difference of the PES and -TDeltaS as a function of the reaction coordinate. For all reactions, it is found that the TS shifts toward the complexation product with increasing temperature because of the curvature increase of -TDeltaS. The equilibrium bond distances for the inactive coordinates perpendicular to the reaction coordinate always increase with temperature, which is due to the thermal excitation and anharmonicity of the PES.

Journal Article↗

Interspecific Competition, Environmental Gradients, Gene Flow, and the Coevolution of Species' Borders.

Darwin viewed species range limits as chiefly determined by an interplay between the abiotic environment and interspecific interactions. Haldane argued that species' ranges could be set intraspecifically when gene flow from a species' populous center overwhelms local adaptation at the periphery. Recently, Kirkpatrick and Barton have modeled Haldane's process with a quantitative genetic model that combines density-dependent local population growth with dispersal and gene flow across a linear environmental gradient in optimum phenotype. To address Darwin's ideas, we have extended the Kirkpatrick and Barton model to include interspecific competition and the frequency-dependent selection that it generates, as well as stabilizing selection on a quantitative character. Our model includes local population growth, movements over space, natural selection, and gene flow. It simultaneously addresses the evolution of character displacement and species borders. It reproduces the Kirkpatrick and Barton single-species result that limited ranges can be produced with sufficiently steep environmental gradients and strong dispersal. Further, in the absence of environmental gradients or barriers to dispersal, interspecific competition will not limit species ranges at evolutionary equilibrium. However, interspecific competition can interact with environmental gradients and gene flow to generate limited ranges with much less extreme gradient and dispersal parameters than in the single-species case. Species display character displacement in sympatry, yet the reduction in competition that results from this displacement does not necessarily allow the two species to become sympatric everywhere. When species meet, competition reduces population densities in the region of overlap, which, in turn, intensifies the asymmetry in gene flow from center to margin. This reduces the ability of each species to adapt to local physical conditions at their range limits. If environmental gradients are monotonic but not linear, the transition zone between species at coevolutionary equilibrium occurs where the environmental gradient is steepest. If productivity gradients are also introduced into the model, then patterns similar to Rapoport's rule emerge. Interacting species respond to climate change, as it affects the optimal phenotype over space, by a combination of range shifts and local evolution in mean phenotype, while solitary species respond solely by range shifts. Finally, we compare empirical estimates for intrinsic growth rates and diffusion coefficients for several species to those needed by the single-species model to produce a stable limited range. These empirical values are generally insufficient to produce limited ranges in the model suggesting a role for interspecific interactions.

Journal Article↗

Pepsin as a catalyst of peptide synthesis. Enzyme co-precipitation with emerging peptide products.

Pepsin successfully catalyzed the synthesis of several peptide derivatives from N-protected di- or tripeptides and amino acid or peptide esters or p-nitroanilides in dimethylformamide-water solutions at pH 4.6. An optimal substrates:pepsin ratio depended on the structure of starting peptides, especially their fit to the substrate binding sites of the enzyme. For hexapeptide Z-Ala-Ala-Phe-Leu-Ala-Ala-OCH3 formation, an equilibrium yield was attained at 1:3.10(5) enzyme-substrates ratio that indicated high efficiency of pepsin in synthesis reactions. In the course of the equilibrium peptide synthesis, pepsin gradually disappeared from the liquid phase due to its entrapment within a gel, formed by the hexapeptide product, while retaining its activity. The inclusion into the precipitate was not specific for pepsin, so far as inert proteins, lysozyme, ribonuclease A and carbonic anhydrase, when added to the reaction mixture, became also co-precipitated with the hexapeptide formed. It appears that co-precipitation of pepsin, an important factor limiting the enzyme efficiency, might be operative as well for other proteinases used to catalyze peptide synthesis.

Amino Acid Sequence↗

Two-hour assay for lutropin during ovulation.

A rapid lutropin assay with a 2-h incubation time and a second antibody/polyethylene glycol separation step is presented. Assay time is shortened by incubating at 37 degrees C and using relatively high concentrations of antibody and radioligand. The interval required for the antigen/antibody reaction varies directly with lutropin concentration, from 1 h for ovulation values to 8 h for low values. After a 2-h incubation, low concentrations have reached 80% of their equilibrium concentration. Separation of the bound fraction by use of combined second antibody/polyethylene glycol (50 g/L) gave one-third the nonspecific binding and as rapid a separation as with polyethylene glycol (180 g/L) alone. Optimal conditions for separating the immune complex were established, and separation was found to be independent of protein concentrations in urine or serum. This tested assay can detect increasing and ovulatory lutropin concentrations in urine or serum, but with some sacrifice in sensitivity.

Female↗

Optimizing protein crystal growth through dynamic seeding.

A dynamic seeding method that is different from the conventional method of seeding drops that have been equilibrated is described. The method basically consists of two steps. Firstly, microseeding was used in association with adjustment of the seeding-drop components, including buffer, additive and concentrations of the precipitants and protein, in order to screen suitable seeding conditions under which microseeds are seeded into a new non-equilibrated drop as the dynamic macroseed drop for the following step. Secondly, after being equilibrated for various times against the reservoir solution, the macroseed drops were used to prepare a dilution series with which the qualified crystals could be harvested using macroseeding. Compared with a conventional seeding technique, this method is distinct with a dynamic situation of macroseed drops before macroseeding and a non-equilibrium serial seeding where all the seeds are seeded into new non-equilibrated drops and the micro/macroseeding are efficiently combined into a whole system. The method simplifies control of the number of microseeds because an excess of microseeds has little effect on the final result. The method also simplifies the manipulation of macroseeds by optimizing the equilibration time and the dilution multiple of the macroseed drops before macroseeding. This dynamic seeding technique has been used in the crystallization of novel protein CutCm, which has a fast crystal-growth rate, and proved that the method is useful for optimizing protein crystallization.

Bacterial Proteins↗