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PubMed2003

Characterization of electronic structure and properties of a Bis(histidine) heme model complex.

Ferric and ferrous hemes, such as those present in electron transfer proteins, often have low-lying spin states that are very close in energy. To explore the relationship between spin state, geometry, and cytochrome electron transfer, we investigate, using density functional theory, the relative energies, electronic structure, and optimized geometries for a high- and low-spin ferric and ferrous heme model complex. Our model consists of an iron-porphyrin axially ligated by two imidazoles, which model the interaction of a heme with histidine residues. Using the B3LYP hybrid functional, we found that, in the ferric model heme complex, the doublet is lower in energy than the sextet by 8.4 kcal/mol and the singlet ferrous heme is 6.7 kcal/mol more stable than the quintet. The difference between the high-spin ferric and ferrous model heme energies yields an adiabatic electron affinity (AEA) of 5.24 eV, and the low-spin AEA is 5.17 eV. Both values are large enough to ensure electron trapping, and electronic structure analysis indicates that the iron d(pi) orbital is involved in the electron transfer between hemes. Mössbauer parameters calculated to verify the B3LYP electronic structure correlate very well with experimental values. Isotropic hyperfine coupling constants for the ligand nitrogen atoms were also evaluated. The optimized geometries of the ferric and ferrous hemes are consistent with structures from X-ray crystallography and reveal that the iron-imidazole distances are significantly longer in the high-spin hemes, which suggests that the protein environment, modeled here by the imidazoles, plays an important role in regulating the spin state. Iron-imidazole dissociation energies, force constants, and harmonic frequencies were calculated for the ferric and ferrous low-spin and high-spin hemes. In both the ferric and the ferrous cases, a single imidazole ligand is more easily dissociated from the high-spin hemes.

Hemeproteins↗

PubMed1999

Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction.

With the objective of improving side-chain conformation prediction, we have analyzed the influence of various factors on prediction by the Self-Consistent Mean Field Theory method, applied to a set of high resolution x-ray protein structure models. These factors may be classed as variations in the mean field optimization protocol, variations in the potential energy function, and variations in rotamer library completeness. We have developed an optimization protocol that consistently reached lower mean field conformational free energies than two other protocols. This protocol led to an important improvement in prediction. We observed a major improvement in prediction with two more detailed van der Waals parameter sets, which we found to be due mainly to the introduction of scaling of 1-4 interactions. In a comparison of two knowledge-based rotamer libraries of considerably different size, we observed an unexpected decrease in prediction with an increase in library completeness. However, when we introduced a torsion potential term in the potential energy function, we found an important increase in average prediction and in the prediction of almost all residue types with a more complete rotamer set. The two knowledge-based rotamer libraries now became equivalent in terms of average prediction. The results we obtained in an analysis of the effect of the introduction of an additional electrostatic term in the potential energy function were largely inconclusive. However, we found a small increase in average prediction for an electrostatic potential term with a fixed dielectric constant of 15. The combined effect of all the factors we analyzed in this study resulted in average prediction accuracies of 79.9% for X1, 68.1% for X1 + 2, and 1.590 A for global rms deviation (RMSD); the corresponding values for core residues were 88.2%, 78.6%, and 1.171 A. These values represent improvements in average prediction of 6.5% for X1, 9.1% for X1 + 2, and 0.163 A for global RMSD over the original conditions; the corresponding improvements in the core were 5.9%, 9.0%, and 0.180 A, respectively.

Amino Acids↗

PubMed1985

Regulation of the degree of coupling of oxidative phosphorylation in intact rat liver.

The degree of coupling of oxidative phopshorylation q was determined in isolated perfused livers and in livers in vivo from fed and fasted rats. This determination of q was based on a simple nonequilibrium-thermodynamic representation of the major reactions of cytosolic adenine nucleotides, and made use of the measured cytosolic concentrations of adenine nucleotides, phosphate, and lactate/pyruvate ratios in extracted livers. The deviations of the measured values from the theoretically predicted ones at different mass action ratios of the adenylate kinase reaction showed that the basic assumptions of the model, including linearity between flows and thermodynamic forces, were fulfilled in intact liver within the experimental error. The degree of coupling was higher in livers from fed rats than in livers from fasted rats. In particular, the determined values of q were close to the theoretical degrees of coupling qecp and qecf which allow maximization of output power and output flow of oxidative phosphorylation for fed and fasted states, respectively, at optimal efficiency and minimal energy costs. This finding indicates that conductance matching between the load and phosphorylation is fulfilled in vivo. Moreover, it was found that fatty acids lower the degree of coupling in a concentration-dependent manner. This suggested that in livers in the fasted state q is decreased due to elevated fatty-acid levels. Thus fatty acids could act as metabolic regulators of the degree of coupling, enabling the cell to optimize efficiency of oxidative phosphorylation under different metabolic regimes.

Adenine Nucleotides↗

PubMed2001

Synthesis and structure of, and bonding in some derivatives of 2,6,9,10-tetraoxatricyclo[3.3.1.1(3,8)]-decane.

Five derivatives of 2,6,9,10-tetraoxatricyclo[3.3.1.1(3,8)]decane were synthesized and their molecular structures in the solid state were determined by means of X-ray diffraction analysis. In addition, the structures of all the molecules were optimized at different levels of computational quantum chemistry (HF/6-31G*, B3LYP/6-31G*). Experimentally determined bond lengths were compared with their calculated counterparts, and striking differences between the Hartree-Fock (HF) results and the experimental data could be traced back to the lack of correlation energy in the geometry optimizations. Two of the compounds under consideration are diastereomers and their relative stability was not only calculated with a conventional ab initio method (ZPE+MP2/6-31G*//HF/6-31G*), but also within the framework of density functional theory (B3LYP/6-31G*). In some of the calculations the influence of the solvent was included in single point calculations by means of an electrostatic model. Moreover, combining experimental as well as computational results, the exclusive axial orientation of a Cl atom in one of the compounds could be explained by an interplay of kinetic and energetic effects.

Journal Article↗

PubMed2005

3-D deformable image registration: a topology preservation scheme based on hierarchical deformation models and interval analysis optimization.

This paper deals with topology preservation in three-dimensional (3-D) deformable image registration. This work is a nontrivial extension of, which addresses the case of two-dimensional (2-D) topology preserving mappings. In both cases, the deformation map is modeled as a hierarchical displacement field, decomposed on a multiresolution B-spline basis. Topology preservation is enforced by controlling the Jacobian of the transformation. Finding the optimal displacement parameters amounts to solving a constrained optimization problem: The residual energy between the target image and the deformed source image is minimized under constraints on the Jacobian. Unlike the 2-D case, in which simple linear constraints are derived, the 3-D B-spline-based deformable mapping yields a difficult (until now, unsolved) optimization problem. In this paper, we tackle the problem by resorting to interval analysis optimization techniques. Care is taken to keep the computational burden as low as possible. Results on multipatient 3-D MRI registration illustrate the ability of the method to preserve topology on the continuous image domain.

Algorithms↗

PubMed2001

Tocqueville revisited. The meaning of American prosperity.

Why is business so admired in the United States and so often denigrated in Europe? How has America created 30 million new jobs in the last 20 years while the European Union, with a bigger population, only managed 5 million? What is feeding America's apparently inexhaustible appetite for growth and its recent dramatic improvements in productivity? In 1831, French philosopher Alexis de Tocqueville came to America to examine its prison system and returned with a vision of democracy so profound it has become part of our cultural heritage. More than a century and a half later, renowned British business philosopher Charles Handy retraces Tocqueville's intellectual journey, this time focusing not on democracy but on capitalism. The result is an eye-opening look at some of the fundamental assumptions underpinning business in America today. It is America's optimism that Handy finds most striking, the unquestioned belief that tomorrow can--and should--be made better than today. He contrasts this with the Spaniards when they came to the New World: No haya novedades, those Spaniards would say, "Let nothing new arise." The energy engendered by American optimism, coupled with the Puritan belief in work and in the nobility of earned wealth (as opposed to Europe's furtive attitude toward its nobility's inherited wealth) lies, in Handy's view, at the heart of America's success. Will American capitalism, born as it was from a property-owning democracy, now adapt to a dematerialized world, where property is intellectual rather than physical? Handy draws no absolute conclusions, but rather lays out the challenges that must be overcome for tomorrow to indeed continue to be better than today in this still-young country.

Commerce↗

PubMed2006

The transition state for formation of the peptide bond in the ribosome.

Using quantum mechanics and exploiting known crystallographic coordinates of tRNA substrate located in the ribosome peptidyl transferase center around the 2-fold axis, we have investigated the mechanism for peptide-bond formation. The calculation is based on a choice of 50 atoms assumed to be important in the mechanism. We used density functional theory to optimize the geometry and energy of the transition state (TS) for peptide-bond formation. The TS is formed simultaneously with the rotatory motion enabling the translocation of the A-site tRNA 3' end into the P site, and we estimated the magnitude of rotation angle between the A-site starting position and the place at which the TS occurs. The calculated TS activation energy, E(a), is 35.5 kcal (1 kcal = 4.18 kJ)/mol, and the increase in hydrogen bonding between the rotating A-site tRNA and ribosome nucleotides as the TS forms appears to stabilize it to a value qualitatively estimated to be approximately 18 kcal/mol. The optimized geometry corresponds to a structure in which the peptide bond is being formed as other bonds are being broken, in such a manner as to release the P-site tRNA so that it may exit as a free molecule and be replaced by the translocating A-site tRNA. At TS formation the 2' OH group of the P-site tRNA A76 forms a hydrogen bond with the oxygen atom of the carboxyl group of the amino acid attached to the A-site tRNA, which may be indicative of its catalytic role, consistent with recent biochemical experiments.

Crystallography, X-Ray↗

PubMed2000

Computational studies on carbohydrates: in vacuo studies using a revised AMBER force field, AMB99C, designed for alpha-(1-->4) linkages.

Modifications to the AMBER force field [W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K. Merz, D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, P.A. Kollman, J. Am. Chem. Soc., 117 (1995) 5179-5197] have been made to improve our ability to reproduce observed molecular properties of alpha-linked carbohydrates when calculated using empirical potential-energy functions. Molecular structures and energies obtained using gradient-optimized density functional methods with ab initio basis sets (B3LYP/6-31G*) on ten minimum-energy conformations of maltose [F.A. Momany, J.L. Willett, J. Comp. Chem., submitted for publication] were used to refine the empirical potentials. Molecular dynamics simulations on beta-maltose (i.e., the beta anomer of maltose), cyclohexamylose (alpha-cyclodextrin), cycloheptamylose (beta-cyclodextrin) and larger cyclomaltooligosaccharide structures were carried out and compared with experimental structural studies to test the new potentials. Ring-puckering potential during dynamics as well as conformational transitions to 'flipped' structures were examined. Results of the tests described here suggest that the revised AMBER parameters (AMB99C) are very good for computational studies of alpha-(1-->4)-linked carbohydrates.

Amylose↗

PubMed2000

Theoretical study of the structure and vibrational spectra of the Ci(2) conformation of 18-crown-6.

Optimized geometries of 18-crown-6 (18ce6) were calculated at the HF/6-31G* and B3LYP/6-31G* levels of theory for the D3d, Ci(1) and Ci(2) conformations. At the B3LYP level, the Ci(2) optimized geometry was higher in energy by 23.3 and 18.8 kcal mol(-1) than the Ci(1) and D3d optimized geometries, respectively. Harmonic force field, vibrational frequencies and IR absorption intensities were calculated at the corresponding optimized geometry at the B3LYP level for the Ci(2) conformation. Scaled Ci(2) frequencies were compared with the experimental frequencies of free 18ce6, Ci(1) conformation, and 18ce6-urea complex, Ci(2) conformation. This comparison showed possible misassignments in the fundamental vibrational frequencies of 18ce6.

Crown Ethers↗

PubMed2005

Density functional theory investigation of Eu(III) complexes with beta-diketonates and phosphine oxides: model complexes of fluorescence compounds for ultraviolet LED devices.

The density functional theory was employed to investigate Eu(III) complexes with three beta-diketonates and two phosphine oxides (complex M1: Eu(bdk)3(TPPO)2, complex M2: Eu(bdk)3(TMPO)2, and complex M3: Eu(bdk)3(TPPO)(TMPO)) deemed to be the model complexes of the fluorescence compounds for the ultraviolet LED devices we have recently developed. For each complex, two minimum energy points corresponding to two different optimized geometries (structures A and B) have been found, and the difference of the energy between two minimum energy points is found to be quite small (less than 1 kcal/mol). Vertical excitation energies and oscillator strengths for each complex at two optimized geometries have been obtained by the time-dependent density functional theory, and the character of the excited states has been investigated. For complex M3, the absorption edge is red-shifted, and the oscillator strengths are relatively large. The efficiency of intersystem crossing and energy transfer from the triplet excited state to the Eu(III) ion is considered by calculating DeltaE(ISC) (the energy difference between the first singlet excited state and the first triplet excited state) and DeltaE(ET) (the difference between the excitation energy of the complex for the first triplet excited state and the emission energy of the Eu(III) ion for 5D to 7F).

Journal Article↗

PubMed1991

Pericardial influence on internal defibrillation energy requirements.

There is no consensus regarding optimal positioning of patch leads for implantation of automatic implantable cardioverter defibrillators. We compared the energy (in joules) required for 50% and 80% successful termination of ventricular fibrillation with titanium-mesh patch leads outside intact normal pericardium and directly on the epicardium in 13 open-chest dogs. Talc was then instilled into the pericardial space to stimulate adhesion formation and pericardial thickening. After 3 weeks of recovery, thoracotomy and defibrillation testing were repeated in nine dogs with the patch leads outside the thickened, adherent pericardium. There were no significant differences in defibrillation energy requirements between locations (p greater than 0.10). In addition, a comparison of electrical impedance measurements at 10 joules showed no significant differences (p greater than 0.30). In this animal model, defibrillation energy requirements were not altered by positioning the patch leads outside normal intact pericardium rather than placing them directly on the epicardium. Furthermore, thickened, adherent pericardium interposed between the patch leads and the heart does not increase defibrillation energy requirements. These data suggest that placement of automatic implantable cardioverter defibrillator patch leads outside the pericardium in patients (including those with pericardial adhesions from previous cardiac operations) will not adversely affect defibrillation efficacy and thus can simplify the implantation procedure.

Animals↗

PubMed1993

Conformations of disaccharides by empirical force field calculations. Part V: Conformational maps of beta-gentiobiose in an optimized consistent force field.

A recently optimized set of potential energy functions is used to investigate the conformational flexibility of the beta-(1-->6) glycosidic linkage in beta-gentiobiose. Relaxed Ramachandran maps in vacuo are presented in the torsional angles phi and omega, with torsional angle psi allowed to relax freely, as are all other internal degrees of freedom. The study reveals two almost iso-energetic low energy domains in (phi, psi, omega) space, and cross-sections in the low-energy domains at omega = -60 degrees and omega = 60 degrees show that more than 60% and 70% respectively of the area of the conformational maps are accessible within 40 kJ mol-1. The molecular structure in the crystal, including the exoanomeric effect, is well reproduced. The structure belongs to the potential energy well which includes the global potential energy minimum in vacuo. The most profound structural difference between the crystal structure and the calculated global minimum in vacuo is the 20 degrees deviation of the psi torsional angle (24 degrees from perfect trans). It occurs in the most flexible glucosidic degree of freedom, psi, and is caused by optimization of the hydrogen bonding network and not by the exoanomeric effect.

Carbohydrate Conformation↗

PubMed2002

Photodissociation of acetic acid in the gas phase: an ab initio study.

Photodissociation of acetic acid in the gas phase was investigated using ab initio molecular orbital methods. The stationary structures on the ground-state potential energy surfaces were mainly optimized at the MP2 level of theory, while those on the excited-state surfaces were determined by complete active space SCF calculations with a correlation-consistent basis set of cc-pVDZ. The reaction pathways leading to different photoproducts are characterized on the basis of the computed potential energy surfaces and surface crossing points. The calculations reproduce the experimental results well and provide additional insight into the mechanism of the ultraviolet photodissociation of acetic acid and related compounds.

Journal Article↗

PubMed1991

Simulated annealing approach to the study of protein structures.

One of the most difficult problems in predicting the three dimensional structure of proteins is how to deal with the local minimum problem. In many cases of practical interest this problem has been reduced to how to select an appropriate set of starting conformations for carrying out energy minimizations. How these starting conformations are selected, however, is often based on the physical intuition of the person doing the calculations, and hence it is hard to avoid bearing some sort of arbitrariness. To improve such a situation, we introduced the simulated annealing Monte Carlo algorithm to locate the optimal starting conformations for energy minimizations. The method developed here is valid for both single and multiple polypeptide chain systems. The annealing process can be conducted with respect to either the internal dihedral angles of a polypeptide chain or the external rotations and translations of various constituent polypeptide chains, and hence is particularly useful for studying the packing arrangements of secondary structures in proteins, such as helix/helix packing, helix/sheet packing and sheet/sheet packing. It was shown via a number of comparative calculations that the final structures obtained through the annealing process not only had lower energies than the corresponding energy-minimized structures reported previously, but also assumed the forms closer to the observations in proteins. All these results indicate that a better result can be obtained in search of low-energy structures of proteins by incorporating the simulated annealing approach.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗

PubMed2000

A priori crystal structure prediction of native celluloses.

The packing of beta-1,4-glucopyranose chains has been modeled to further elaborate the molecular structures of native cellulose microfibrils. A chain pairing procedure was implemented that evaluates the optimal interchain distance and energy for all possible settings of the two chains. Starting with a rigid model of an isolated chain, its interaction with a second chain was studied at various helix-axis translations and mutual rotational orientations while keeping the chains at van der Waals separation. For each setting, the sum of the van der Waals and hydrogen-bonding energy was calculated. No energy minimization was performed during the initial screening, but the energy and interchain distances were mapped to a three-dimensional grid, with evaluation of parallel settings of the cellulose chains. The emergence of several energy minima suggests that parallel chains of cellulose can be paired in a variety of stable orientations. A further analysis considered all possible parallel arrangements occurring between a cellulose chain pair and a further cellulose chain. Among all the low-energy three-chain models, only a few of them yield closely packed three-dimensional arrangements. From these, unit-cell dimensions as well as lattice symmetry were derived; interestingly two of them correspond closely to the observed allomorphs of crystalline native cellulose. The most favorable structural models were then optimized using a minicrystal procedure in conjunction with the MM3 force field. The two best crystal lattice predictions were for a triclinic (P(1)) and a monoclinic (P2(1)) arrangement with unit cell dimensions a = 0.63, b = 0.69, c = 1.036 nm, alpha = 113.0, beta = 121.1, gamma = 76.0 degrees, and a = 0.87, b = 0.75, c = 1.036 nm, gamma = 94.1 degrees, respectively. They correspond closely to the respective lattice symmetry and unit-cell dimensions that have been reported for cellulose Ialpha and cellulose Ibeta allomorphs. The suitability of the modeling protocol is endorsed by the agreement between the predicted and experimental unit-cell dimensions. The results provide pertinent information toward the construction of macromolecular models of microfibrils.

Carbohydrate Conformation↗

PubMed1990

Wound healing and the aged patient.

The aged patient is more susceptible to wound healing problems because of the interactions of body systems, environmental stresses, and disease with an aging process that takes place over many years. The multifactorial nature of wound healing in the elderly makes it difficult to determine whether observed healing problems are attributable to results of aging or other factors. Healing is affected by multiple factors in addition to patient age, which itself is not a dependable indicator of physiologic health. Some of these factors are disease, nutrition, perfusion, skin quality, environment, and individual responses to life events. It is particularly difficult for the aged patient to sustain the motivation to participate in care required during the healing process when cascading problems are allowed to build on the decreasing functions and reserve capacities of aging body systems and deplete available energy levels. Assessment of each individual is required because of the wide variety of aging changes and healing responses seen in aged patients. Compared with a younger adult, the aged patient generally heals well, following the same healing process but at a slower rate. Wound healing for the aged can be optimized through techniques of energy conservation, correction of existing problems, and management of risks related to aging and the individual patient. Healing problems are usually the result of decreases in systemic and local perfusion, decreases in the ability to ward off infection, and fragility of aging skin. The aged patient requires the same care as younger patients. It is more critical that this care be meticulously delivered with particular attention to care of intact skin, effects of chronic disease and medications, motivation, social habits, and discharge planning. Nurses can promote improved healing through the care they provide and by studying the progression of healing in aged patients.

Aged↗

PubMed2004

Optimization of the extraction of paclitaxel from Taxus baccata L. by the use of microwave energy.

A simple and rapid microwave-assisted extraction (MAE) procedure was developed and optimized for the extraction of paclitaxel (Taxol) from the needles of yew trees Taxus baccata L. grown in Iranian habitats. The samples, immersed in a methanol-water mixture, were irradiated with microwaves in a closed-vessel system. The method was evaluated using a factorial design approach based on parameters such as extraction time, temperature, methanol concentration in water (v/v), and the ratio of grams of sample to 10 mL of solvent. Statistical treatment of the results revealed that the selected parameters were all significant except the extraction time. Optimum conditions would be 1.5 g samples in 10 mL solvent (90% methanol), an extraction temperature of 95 degrees C, and an extraction time of 7 min. The extracts has been analyzed by reverse-phase high-performance liquid chromatography with UV detection (LC/UV) at 227 nm for quantification. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used for confirmation. The main advantage of the proposed MAE method versus conventional solvent extraction (CSE) are the considerable reductions in time (7 min versus 16 h) and in solvent consumption (20 mL versus 150 mL). The MAE procedure yielded extracts that could be analyzed directly without any preliminary clean-up or solvent exchange steps. Both extraction methods show RSDs lower than 10% and lead to comparable recoveries of paclitaxel (87-92%).

Chromatography, High Pressure Liquid↗

PubMed2005

Energy demand in sludge dewatering.

This work investigates the energy required to dewater a suspension, i.e., activated sludge dewatered by centrifugation or consolidation. Total energy input to the suspension from the dewatering device, bond strength between adjacent water and solid surface, and intra-cake friction loss were evaluated for original and flocculated sludges. In centrifugal dewatering, most energy input during the initial stage was consumed by overcoming process irreversibility other than intra-cake friction, and, thereby, had a low energy efficiency. To increase centrifuge speed or to flocculate the sludge at optimal flocculant dosage would yield a high-energy input. In the consolidation test, most energy input at the initial stage was consumed in breaking down the bond strength until the moisture content reduced to less than the critical content. During subsequent dewatering stages, friction loss became the dominant source of energy loss. Dewatering sludge with high-energy efficiency is beneficial to optimally operate a dewatering process.

Centrifugation↗