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PubMedDate not supplied

Parameters for and safety of contact Nd:YAG laser irradiation of early gastric cancer: an in vitro study.

Early gastric cancers have been treated by endoscopic contact Nd:YAG laser irradiation. The extent of thermal damage produced by this laser system has been inadequately investigated. In an in vitro study we have shown that contact laser probes produce consistent and reproducible thermal lesions in the human stomach wall. Contact laser energies of 40 to 60 joules are optimal for the ablation of early gastric cancer. Energies greater than 90 joules are associated with a high incidence of gastric perforation. Contact laser probes may have advantages over non-contact laser techniques for the endoscopic treatment of early gastric cancer in patients who are unfit for major surgery.

Adenocarcinoma↗

PubMedDate not supplied

[Energy expenditures and the actual nutrition of workers in a synthetic leather plant].

A study was made of energy expenditures and factual nutrition of the workers engaged in synthetic leather manufacture. Antropometric measurements were also taken. Based on the study of daily energy expenditures, the calculations were made of the optimal requirements of the main substances and energy. The actual nutrition of the workers was found to provide the necessary caloricity covering energy expenditures. However, definite shortcomings were revealed in the structure of the foods consumed, namely insufficient intake of vegetable fats, the prevalence of simple sugars in the structure of carbohydrate component, insufficient intake of vitamins A, B1 and folacin. According to the antropometric measurements 30,4% of the examined workers were obese.

Adult↗

PubMed1988

Coordination in vertical jumping.

The present study was designed to investigate for vertical jumping the relationships between muscle actions, movement pattern and jumping achievement. Ten skilled jumpers performed jumps with preparatory countermovement. Ground reaction forces and cinematographic data were recorded. In addition, myoelectric activity (EMG) was recorded from seven leg muscles. EMG-signals were rectified and low-pass filtered to obtain EMG-levels. The latter, which were assumed to reflect activation levels, rose to a plateau in the sequence m. semitendinosus, long head of m. biceps femoris, m. gluteus maximus, m. vastus medialis, m. rectus femoris, m. soleus, m. gastrocnemius. It was attempted to link the EMG-pattern to the purpose of the push-off, namely to maximize the effective energy (Ey) of the mass center of the body (MCB). The term Ey designates the sum of the potential energy of MCB and the kinetic energy due to the vertical velocity of MCB. One of the requirements for maximization of Ey is that the mono-articular extensor muscles release as much energy as possible before toe-off occurs. It is argued that this requirement can only be satisfied if the vertical velocity differences between the proximal and distal ends of body segments reach their peaks in a sequence. The sequence that is realized by the pattern of muscular activation is upper body, upper legs, lower legs, feet. Another important requirement is that the mechanical energy released by the muscles is optimally used. This requirement can be satisfied by transportation of energy via the biarticular m. rectus femoris and m. gastrocnemius.

Biomechanical Phenomena↗

PubMed1985

Control of Oxidative Sulfur Metabolism of Chlorobium limicola forma thiosulfatophilum.

A metered blend of anaerobic-grade N(2), CO(2), and H(2)S gases was introduced into an illuminated, 800-ml liquid volume, continuously stirred tank reactor. The system, described as an anaerobic gas-to-liquid phase fed-batch reactor, was used to investigate the effects of H(2)S flow rate and light energy on the accumulation of oxidized sulfur compounds formed by the photoautotroph Chlorobium limicola forma thiosulfatophilum during growth. Elemental sulfur was formed and accumulated in stoichiometric quantities when light energy and H(2)S molar flow rate levels were optimally adjusted in the presence of nonlimiting CO(2). Deviation from the optimal H(2)S and light energy levels resulted in either oxidation of sulfur or complete inhibition of sulfide oxidation. Based on these observations, a model of sulfide and sulfur oxidases electrochemically coupled to the photosynthetic reaction center of Chlorobium spp. is presented. The dynamic deregulation of oxidative pathways may be a mechanism for supplying the photosynthetic reaction center with a continuous source of electrons during periods of varying light and substrate availability, as in pond ecosystems where Chlorobium spp. are found. Possible applications for a sulfide gas removal process are discussed.

Journal Article↗

PubMed1982

Conformational-energy studies of tetrapeptide opiates. Candidate active and inactive conformations.

The conformational behavior of four tetrapeptide enkephalin analogues (Tyr-Gly-Gly-Phe-OH, Tyr-Gly-Gly-Phe-NH2, Tyr-D-Ala-Gly-Phe-NH2, and Tyr-D-Ala-Gly-(NMe)Phe-NH2) was examined to identify conformations that are active and inactive at the opiate analgesic receptor. By using an empirical energy program, conformational energies were obtained for the optimized geometries of each tetrapeptide. Two methods of selecting candidate active conformations from low-energy conformers were used. In the first method, inactive conformers were designated as low-energy conformations of the very weak tetrapeptide, Tyr-Gly-Gly-Phe-OH. These candidate inactive conformers had geometries resembling beta V, beta I, "random" peptide conformations. Candidate active conformers selected were low-energy conformations found for both Tyr-D-Ala-Gly-Phe-NH2 and Tyr-D-Ala-Gly-(NMe)Phe-NH2 but not low-energy conformers for Tyr-Gly-Gly-Phe-OH. In the second method of selection, conformers with relative energies in the active and inactive peptides that followed the potency order Tyr-Gly-Gly-Phe-OH much less than Tyr-D-Ala-Gly-Phe-NH2 less than or equal to Tyr-D-Ala-Gly-(NMe)Phe-NH2 were chosen as candidate active conformers. By using both methods of selection, a beta II' bend geometry was found as the active conformer. This beta II' conformer was not stabilized by a 1-4 hydrogen bond, but instead was stabilized by a hydrogen bond between the tyrosine amine hydrogen atom and the phenylalanine carbonyl oxygen atom. The effect of C-terminal amide derivitization on peptide conformation was also examined by comparing the conformational profiles of Tyr-Gly-Gly-Phe-OH and Tyr-D-Ala-Gly-Phe-OH with their amides Tyr-Gly-Gly-Phe-OH-NH2 and Tyr-D-Ala-Gly-Phe-NH2. No significant difference in conformational behavior was found for the Tyr-Gly-Gly-Phe pair; however, a difference in conformational behavior was found between the Tyr-D-Ala-Gly-Phe acid and amide. Thus, on the basis of conformational data, the Tyr-Gly-Gly-Phe-NH2 analogue is predicted to have very weak opiate activity.

Amino Acid Sequence↗

PubMed1999

Sperm metabolism of the telost fishes Chalcalburnus chalcoides and Oncorhynchus mykiss and its relation to motility and viability.

In the teleost fish Chalcalburnus chalcoides (Cyprinidae) the influence of metabolic inhibitors, substrates, coenzymes, and oxygen concentrations on spermatozoal parameters during motility and during immotile incubation was studied, the respiration rate was characterized, representative metabolite levels were measured, and the results were compared with Oncorhynchus mykiss (Salmonidae). In Chalcalburnus chalcoides the sperm motility rate, the average path swimming velocity, the motility duration, and the viability of immotile semen were significantly reduced in the presence of inhibitors of respiration (potassium cyanide, 2.4-dinitrophenol, atractyloside). Anaerobic conditions (<1 mg O(2)/liter) and inhibition of the tricarboxylic acid cycle by malonate and >7.5 mmol/liter succinate had similar effects on the sperm motility parameters and on the viability of immotile spermatozoa. Pyruvate and coenzyme A (an acyl-group carrier during oxidative carboxylation of pyruvate) prolonged the duration of sperm motility and the viability of immotile incubated spermatozoa, and also increased the spermatozoal respiration rate. Glucose levels significantly decreased during motility and during immotile storage and, under anaerobic conditions, the levels of lactate increased indicating that pyruvate derived from glycolysis. The respiration rate and the glycolytic rate significantly increased during motility. Therefore oxidative phosphorylation, tricarboxylic acid cycle, and aerobic glycolysis are central energy-supplying pathways for spermatozoa of Chalcalburnus chalcoides. The stimulatory effect of pyruvate and coenzyme A indicated that glycolysis is a rate-controlling pathway. Similar results were obtained for Oncorhynchus mykiss with the only exception that the stimulatory effect of coenzyme A was more significant than the stimulatory effect of pyruvate. When the sperm motility-activating saline solutions were optimized in aspects of energy supply, ionic composition, and osmolality, about 50% of the motile spermatozoa swam progressively (>20 mm/sec) for about 3 min in Chalcalburnus chalcoides and in Oncorhynchus mykiss. About 20% swam progressively for >2 hr in Chalcalburnus chalcoides and for >30 min in Oncorhynchus mykiss. J. Exp. Zool. 284:454-465, 1999.

2,4-Dinitrophenol↗

PubMed2006

Calculation of electron deposition in proportional counters.

Efficiency extrapolation is a common technique in the standardization of radionuclides by the technique of 4pibeta-gamma coincidences. It can be achieved in two ways: adding thin films onto the radioactive source or by electronic discrimination in a pressurized 4pibeta-gamma system. The last case is the most extensively used actually in metrology laboratories. There is a need to know the electron energy loss inside the proportional counter as a function of the electron energies and working pressures. Calculations of electron energy loss have been performed for electron energies in a range from a few keV to 2 MeV in a mixture of Ar(90%) CH4(10%) and for pressures ranging from 100 to 2000 kPa in a 5 cm radius proportional counter. Wall effects, such as electron backscattering, are included in the calculations. Results are provided in the form of graphs and some recommendations are given about the optimal values of the energies that can be used to perform the extrapolation in the standardization of some radionuclides.

Algorithms↗

PubMed2003

Evaluation of thyroid function in obese dogs and in dogs undergoing a weight loss protocol.

Obesity and weight loss have been shown to alter thyroid hormone homeostasis in humans. In dogs, obesity is the most common nutritional problem encountered and weight loss is the cornerstone of its treatment. Therefore, it is important to clarify how obesity and weight loss can affect thyroid function test results in that species. The objectives of this study were to compare thyroid function in obese dogs and in lean dogs and to explore the effects of caloric restriction and weight loss on thyroid hormone serum concentrations in obese dogs. In the first experiment, 12 healthy lean beagles and 12 obese beagles were compared. Thyroid function was evaluated by measuring serum concentrations of total thyroxine (TT4), free thyroxine (FT4), total triiodothyronine (TT3), thyrotropin (TSH), and reverse triiodothyronine (rT3) as well as a TSH stimulation test using 75 microg i.v. of recombinant human TSH. In the second experiment, eight obese beagles were fed an energy-restricted diet [average 63% maintenance energy requirement (MER)] until optimal weight was obtained. Blood samples for determination of TT4, FT4, TT3, TSH and rT3, were taken at the start and then weekly during weight loss. Only TT3 and TT4 serum concentrations were significantly higher in obese dogs as compared to lean dogs. In the second experiment, weight loss resulted in a significant decrease in TT3 and TSH serum concentrations. Thus obesity and energy restriction significantly alter thyroid homeostasis in dogs, but the observed changes are unlikely to affect interpretation of thyroid function test results in clinics.

Animals↗

PubMed1995

Predicting free energy contributions to the conformational stability of folded proteins from the residue sequence with radial basis function networks.

Radial basis function neural networks are trained on a data base comprising 38 globular proteins of well resolved crystallographic structure and the corresponding free energy contributions to the overall protein stability (as computed partially from chrystallographic analysis and partially with multiple regression from experimental thermodynamic data by Ponnuswamy and Gromiha (1994)). Starting from the residue sequence and using as input code the percentage of each residue and the total residue number of the protein, it is found with a cross-validation method that neural networks can optimally predict the free energy contributions due to hydrogen bonds, hydrophobic interactions and the unfolded state. Terms due to electrostatic and disulfide bonding free energies are poorly predicted. This is so also when other input codes, including the percentage of secondary structure type of the protein and/or residue-pair information are used. Furthermore, trained on the computed and/or experimental delta G values of the data base, neural networks predict a conformational stability ranging from about 10 to 20 kcal mol-1 rather independently of the residue sequence, with an average error per protein of about 9 kcal mol-1.

Calorimetry↗

PubMed2002

Designing the optimal Total Cavopulmonary Connection: pulsatile versus steady flow experiments.

BACKGROUND: The Total Cavopulmonary Connection (TCPC), used for repair of patients with single ventricle physiology, creates a passive system of blood flow into the pulmonary circulation where enhanced energy efficiency may lead to improved long term patient outcomes. Previous numerical and in vitro studies using steady flow have shown that incorporation of SVC (superior vena cava) and IVC (inferior vena cava) offsets lead to decreased energy losses. We hypothesize that the optimal TCPC offset design found in these previous steady flow experiments may not be the optimal design in pulsatile flow situations. MATERIAL/METHODS: 3-D finite volume numerical models were used to simulate flow through the total cavopulmonary connection. We ran steady and pulsatile flow experiments through 4 TCPC designs each with different SVC to IVC offsets (0.1/4, 1/2, 1 diameter offsets). The total energy (power) loss for each TCPC model was calculated. RESULTS: In steady flow experiments, % difference in energy loss between the most optimal and least optimal design was 26%. In contrast, in pulsatile flow experiments the % difference was only 8%. CONCLUSIONS: Our results demonstrate the improvements in energy loss seen using SVC-IVC offsets in steady flow experiments do not necessarily translate to pulsatile flow situations. Overall there was lower differences in efficiency between all TCPC designs in the pulsatile flow experiments. These results emphasize the need for further studies to fully define the relationship between energy losses and TCPC vessel architecture in non-steady flow physiologic situations.

Blood Flow Velocity↗

PubMed2006

Photoreactions in the gas-phase complexes of Mg(*+)-dioxanes.

Photoreactions in the gas-phase complexes Mg(*+)(1,4-dioxane) (1) and Mg(*+)(1,3-dioxane) (1M) have been examined in the wavelength region of 230-440 nm. Photoproduct assignments are facilitated with the help of deuterium substitution experiments. The main energy relaxation channel for both photoexcited complexes is the evaporation of Mg(*+). Also observed from 1 are rich photoproducts with m/z 28, 41, 54-58, 67, 69, and 88; the most abundant one at m/z 54 is designated to Mg(*+)(O=CH(2)). In marked contrast, the photolysis of 1M yields only Mg(*+)(O=CH(2)) other than Mg(*+). Density functional calculations are performed to obtain optimized geometries and potential energy surfaces of 1 and 1M. Although Mg(*+)(chair-1,4-C(4)H(8)O(2)) (1a) and Mg(*+)(boat-1,4-C(4)H(8)O(2)) (1b) are comparable in energy, the much better agreement of the experimental action spectrum of Mg(*+)(1,4-C(4)H(8)O(2)) with the calculated absorption spectrum of 1a than with that of 1b indicates the predominance of 1a in the source due to the stability of the chair-1,4-dioxane. For photoreactions, the C-O bond is found to be much more prone to rupture than the C-C bond due to the coordination of O to Mg(+) in the parent complexes. Photoreaction mechanisms are discussed in terms of two key insertion complexes, which rationalize all of the observed photoproducts.

Journal Article↗

PubMed2004

[Nutrient and water cycling in red soils with different planting system and their management].

Based on the data of long term located experiment, this paper studied the characteristics of nutrient and water cycling and balance and of energy flow in upland red soils with different planting system. The results showed that in red soil areas, the rainfall from March to June accounted for 60% of the whole year, which induced frequent seasonal drought and severe water and soil loss. The application of N, P and K on upland red soil was overabundant and unbalanced, which induced a reduced ratio of input and output. Optimized planting mode could increase the water and light utilization efficiency, decrease the frequency and degree of occurred drought, and increase the nutrient recycling rate. The main measures for rationally developing and utilizing red soil should be establishing compound agro-ecosystem model of planting and feeding, saving irrigation water, increasing mulch, cover-cultivating crops and forests, increasing the proportion of organic fertilizer, realizing rational and balanced fertilization, further optimizing planting structure, regulating energy input structure, and adopting multilevel-technologies of food chain utilization.

China↗

PubMed1994

Predicting protein mutant energetics by self-consistent ensemble optimization.

In this paper we present a self-consistent ensemble optimization (SCEO) theory for efficient conformational search, which we have applied to predicting the effects of mutations on protein thermostability. This approach takes advantage of a statistical mechanical self-consistency condition to home in iteratively on the global minimum structure. We employ a fast potential of mean-force approximation to cut computation time to a few minutes for a typical protein mutation, with only linear time-dependence on the size of the prediction problem. Rather than seeking a single, static structure of minimum energy, the new method optimizes an ensemble of many conformations, seeking to predict the most likely ensemble for the native state at a desired temperature. Testing this approach with a simple physical model focusing entirely on steric interactions and side-chain rearrangement, we obtain robustly convergent prediction of core side-chain conformation, and of hydrophobic core mutations' effects on protein stability. Self-consistent ensemble optimization is superior to simulated annealing in its speed and convergence to the global minimum, and insensitive to starting conformation. In calculations on lambda repressor protein, structural predictions for an eight-residue molten-zone had side-chain r.m.s. error of 0.49 A for the wild-type protein. Evaluation of the method's mutant structure predictions should become possible, as structures of these mutant repressors are solved. Predicted energies for a series of nine hydrophobic core mutants correlated with measured free energies of unfolding with a coefficient of 0.82.

Amino Acid Sequence↗

PubMed1993

Storage and utilization of elastic strain energy during jumping.

Based upon the optimal control solutions to a maximum-height countermovement jump (CMJ) and a maximum-height squat jump (SJ), this paper provides a quantitative description of how tendons and the elastic elements of muscle store and deliver energy during vertical jumping. After confirming the ability of the model to replicate the major features of each jump (i.e. muscle activation patterns, body-segmental motions, ground reaction forces, jump height, and total ground contact time), the time histories of the forces and shortening velocities of all the musculotendon actuators in the model were used to calculate the work done on the skeleton by tendons as well as the series-elastic elements, the parallel-elastic elements, and the contractile elements of muscle. We found that all the elastic tissues delivered nearly the same amount of energy to the skeleton during a CMJ and an SJ. The reason is twofold: first, nearly as much elastic strain energy was stored during the SJ as the CMJ; second, more stored elastic strain energy was lost as heat during the CMJ. There was also a difference in the way energy was stored during each jump. During the CMJ, strain energy stored in the elastic tissues came primarily from the gravitational potential energy of the skeleton as the more proximal extensor muscles were stretched during the downward phase of the jump. During the SJ, on the other hand, energy stored in the elastic tissues came primarily from the contractile elements as they did work to stretch the tendons and the series-elastic elements of the muscles. Increasing tendon compliance in the model led to an increase in elastic energy storage and utilization, but it also decreased the amount of energy delivered by the contractile elements to the skeleton. Jump height therefore remained almost the same for both jumps. These results suggest that elastic energy storage and utilization enhance jumping efficiency much more than overall jumping performance.

Adult↗

PubMed2005

Stabilization of excess charge in isolated adenosine 5'-triphosphate and adenosine 5'-diphosphate multiply and singly charged anions.

Multiply charged anions (MCAs) represent highly energetic species in the gas phase but can be stabilized through formation of molecular clusters with solvent molecules or counterions. We explore the intramolecular stabilization of excess negative charge in gas-phase MCAs by probing the intrinsic stability of the [adenosine 5'-triphosphate-2H](2-) ([ATP-2H](2-)), [adenosine 5'-diphosphate-2H](2-) ([ADP-2H](2-)), and H(3)P(3)O(10)(2-) dianions and their protonated monoanionic analogues. The relative activation barriers for decay of the dianions via electron detachment or ionic fragmentation are investigated using resonance excitation of ions isolated within a quadrupole trap. All of the dianions decayed via ionic fragmentation demonstrating that the repulsive Coulomb barriers (RCB) for ionic fragmentation lie below the RCBs for electron detachment. Both the electrospray ionization mass spectra (ESI-MS) and total fragmentation energies for [ATP-2H](2-), [ADP-2H](2-), and H(3)P(3)O(10)(2-) indicate that the multiply charged H(3)P(3)O(10)(2-) phosphate moiety is stabilized by the presence of the adenosine group and the stability of the dianions increases in the order H(3)P(3)O(10)(2-) < [ADP-2H](2-) < [ATP-2H](2-). Fully optimized, B3LYP/6-31+G* minimum energy structures illustrate that the excess charges in all of the phosphate anions are stabilized by intramolecular hydrogen bonding either within the phosphate chain or between the phosphate and the adenosine. We develop a model to illustrate that the relative magnitudes of the RCBs and hence the stability of these ions is dominated by the extent of intramolecular hydrogen bonding.

Adenosine Diphosphate↗

PubMed2006

Mathematical modeling of endovenous laser treatment (ELT).

BACKGROUND AND OBJECTIVES: Endovenous laser treatment (ELT) has been recently proposed as an alternative in the treatment of reflux of the Great Saphenous Vein (GSV) and Small Saphenous Vein (SSV). Successful ELT depends on the selection of optimal parameters required to achieve an optimal vein damage while avoiding side effects. Mathematical modeling of ELT could provide a better understanding of the ELT process and could determine the optimal dosage as a function of vein diameter. STUDY DESIGN/MATERIALS AND METHODS: The model is based on calculations describing the light distribution using the diffusion approximation of the transport theory, the temperature rise using the bioheat equation and the laser-induced injury using the Arrhenius damage model. The geometry to simulate ELT was based on a 2D model consisting of a cylindrically symmetric blood vessel including a vessel wall and surrounded by an infinite homogenous tissue. The mathematical model was implemented using the Macsyma-Pdease2D software (Macsyma Inc., Arlington, MA, USA). Damage to the vein wall for CW and single shot energy was calculated for 3 and 5 mm vein diameters. In pulsed mode, the pullback distance (3, 5 and 7 mm) was considered. For CW mode simulation, the pullback speed (1, 2, 3 mm/s) was the variable. The total dose was expressed as joules per centimeter in order to perform comparison to results already reported in clinical studies. RESULTS: In pulsed mode, for a 3 mm vein diameter, irrespective of the pullback distance (2, 5 or 7 mm), a minimum fluence of 15 J/cm is required to obtain a permanent damage of the intima. For a 5 mm vein diameter, 50 J/cm (15W-2s) is required. In continuous mode, for a 3 mm and 5 mm vein diameter, respectively 65 J/cm and 100 J/cm are required to obtain a permanent damage of the vessel wall. Finally, the use of different wavelengths (810 nm or 980 nm) played only a minor influence on these results. DISCUSSION AND CONCLUSION: The parameters determined by mathematical modeling are in agreement with those used in clinical practice. They confirm that thermal damage of the inner vein wall (tunica intima) is required to achieve the tissue alterations necessary in order to lead the vein to permanent occlusion. However, in order to obtain a high rate of success without adverse events, the knowledge of the vein diameter after tumescent anesthesia is recommended in order to use the optimal energy. As clearly demonstrated by our calculations, both pulsed and continuous mode operations of the laser can be efficient. An interesting observation in our model is that less amount of energy is required in pulsed mode than in continuous mode. Damaging the vein sequentially along its entire length may lead to permanent occlusion. However, the pulsed mode requires a very precise positioning of the fiber after each pullback and the duration of the treatment is much longer. For these reasons, continuous irradiation seems to be preferred by most clinicians. This model should serve as a useful tool to simulate and better understand the mechanism of action of the ELT.

Animals↗

PubMed2003

Assessing the performance of OMEGA with respect to retrieving bioactive conformations.

OMEGA is a rule-based program which rapidly generates conformational ensembles of small molecules. We have varied the parameters which control the nature of the ensembles generated by OMEGA in a statistical fashion (D-optimal) with the aim of increasing the probability of generating bioactive conformations. Thirty-six drug-like ligands from different ligand-protein complexes determined by high-resolution (< or =2.0A) X-ray crystallography have been analyzed. Statistically significant models (Q(2)> or =0.75) confirm that one can increase the performance of OMEGA by modifying the parameters. Twenty-eight of the bioactive conformations were retrieved when using a low-energy cut-off (5 kcal/mol), a low RMSD value (0.6A) for duplicate removal, and a maximum of 1000 output conformations. All of those that were not retrieved had eight or more rotatable bonds. The duplicate removal parameter was found to have the largest impact on retrieval of bioactive conformations, and the maximum number of conformations also affected the results considerably. The input conformation was found to influence the results largely because certain bond angles can prevent the bioactive conformation from being generated as a low-energy conformation. Pre-optimizing the input structures with MMFF94s improved the results significantly. We also investigated the performance of OMEGA in connection with database searching. The shape-matching program Rapid Overlay of Chemical Structures (ROCS) was used as search tool. Two multi-conformational databases were built from the MDDR database plus the 36 compounds; one large (maximum 1000 conformations/mol) and one small (maximum 100 conformations/mol). Both databases provided satisfactory results in terms of retrieval. ROCS was able to rank 35 out of 36 X-ray structures among the top 500 hits from the large database.

Algorithms↗

PubMed2007

An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory: application to alanine tetrapeptide conformational analysis.

We present a new algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory (RI-MP2) and thoroughly assess its computational performance and chemical accuracy. This algorithm addresses the potential I/O bottlenecks associated with disk-based storage and access of the RI-MP2 t-amplitudes by utilizing a semi-direct batching approach and yields computational speed-ups of approximately 2-3 over the best conventional MP2 analytical gradient algorithms. In addition, we attempt to provide a straightforward guide to performing reliable and cost-efficient geometry optimizations at the RI-MP2 level of theory. By computing relative atomization energies for the G3/99 set and optimizing a test set of 136 equilibrium molecular structures, we demonstrate that satisfactory relative accuracy and significant computational savings can be obtained using Pople-style atomic orbital basis sets with the existing auxiliary basis expansions for RI-MP2 computations. We also show that RI-MP2 geometry optimizations reproduce molecular equilibrium structures with no significant deviations (>0.1 pm) from the predictions of conventional MP2 theory. As a chemical application, we computed the extended-globular conformational energy gap in alanine tetrapeptide at the extrapolated RI-MP2/cc-pV(TQ)Z level as 2.884, 4.414, and 4.994 kcal/mol for structures optimized using the HF, DFT (B3LYP), and RI-MP2 methodologies and the cc-pVTZ basis set, respectively. These marked energetic discrepancies originate from differential intramolecular hydrogen bonding present in the globular conformation optimized at these levels of theory and clearly demonstrate the importance of long-range correlation effects in polypeptide conformational analysis.

Alanine↗