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PubMed1991

The helix-coil transition in heterogeneous peptides with specific side-chain interactions: theory and comparison with CD spectral data.

Natural and synthetic peptides that contain detectable intramolecular alpha-helical structure in aqueous solution have been used to evaluate the helical propensities for the common amino acids. Experimental spectroscopic data must be fit to a model of the helix-coil transition in order to determine quantitative stability constants for each amino acid. We present here a statistical mechanical description of helix formation in peptides or protein fragments that takes into account multiple internal conformations, heterogeneity in the stabilizing effects of different side chains, and specific side-chain-side-chain interactions. The model enables one to calculate values of [theta]222 for a given peptide using the length dependence of the helix signal computed by a quantum mechanical treatment of the n pi * transition that dominates the 222-nm band. In addition, the helical probability at any residue in the chain is readily computed, and should prove useful as nmr spectral data become available. The free energy of specific side-chain interactions, including ion pair formation, can be evaluated. Application of the analysis to experimental data on a pair of isomeric peptides, only one of which contains ion pairs, indicates that forming a single glutamate-lysine ion pair stabilizes the alpha-helix by 0.50 kcal/mole in 10 mM sodium ion and pH 7. A survey of the CD data measured for a variety of model peptides is presented, indicating that a single set of s values and sigma constant can account for some but not all of the available results.

Amino Acid Sequence↗
PubMed1977

Luminescence quantum yields of sound and carious dental enamel.

The absorption and emission spectra of slabs of human and bovine dental enamel were determined. The absorption and scattering coefficients and emission quantum yields were computed according to theoretical models. The samples were gradually demineralized. The absorption, scattering, and emission parameters were determined as a function of the demineralization time. Using the theoretical models combined with the experimental values, ratio of the visible and UV luminescence, and the decrease of visible emission intensity upon demineralization are explained.

Absorption↗
PubMed1991

Spectrofluorimetric studies on C-terminal 34 kDa fragment of caldesmon.

Analysis of the tryptophan fluorescence emission spectra of caldesmon and its 34 kDa C-terminal fragment indicates that all tryptophan residues are located on the surface of the molecule, accessible to solvent. All three tryptophan residues of the 34 kDa fragment and four of the five tryptophan residues of intact protein are accessible to free water, whereas one located in the N-terminal region of molecule is accessible only to bound water molecules. The temperature dependence of the fluorescence parameters indicates higher thermal stability of the 34 kDa fragment than the whole caldesmon molecule. The interaction of the 34 kDa fragment of caldesmon (like that of the intact molecule) with calmodulin is accompanied by a blue shift of the fluorescence emission maximum and an increase in the relative quantum yield. Computer-calculated binding constants show that the binding of calmodulin to the 34 kDa fragment (K = 2.5 x 10(5) M-1) is of two orders of magnitude weaker than that to intact caldesmon (K = 1.4 x 10(7) M-1). The interaction with tropomyosin results in a blue shift of the spectrum of the 34 kDa fragment, yet there is no effect on the spectrum of intact caldesmon. Binding constants of tropomyosin to caldesmon (K = 3.8 x 10(5) M-1) and its 34 kDa fragment (K = 2.3 x 10(5) M-1) are similar. Binding of calmodulin to caldesmon and to the 34 kDa fragment affects their interaction with tropomyosin.

Animals↗
PubMed1992

Computer simulations of enzymatic reactions: examination of linear free-energy relationships and quantum-mechanical corrections in the initial proton-transfer step of carbonic anhydrase.

Computer simulation approaches can provide a powerful tool for correlating the structure of enzymes with their catalytic activity. One of the most effective ways of simulating enzymatic reactions is provided by the empirical valence bond method. The general applicability of this method has been demonstrated in several enzymatic reactions and it is reexamined here in a study of the initial proton-transfer step in the catalytic reaction of carbonic anhydrase. The simulations produce a rate constant which is in agreement with the observed kinetic data and emphasizes the importance of the electrostatic effect associated with the catalytic zinc ion. The calculations are also used to examine the validity of linear free-energy relationships (LFERs) in enzyme catalysis and to evaluate quantum-mechanical corrections of the calculated rate constant. It is found that LFERs are valid in the present case and it is argued that this reflects the fact that the protein responds linearly to the development of electrostatic forces during the reaction. It is concluded that the present approach can be used to augment experimental studies in establishing the general validity of LFERs. It is noted, however, that such relationships are much more valid for transitions between different resonance structures than for transitions between reactants and product states.

Carbonic Anhydrases↗
PubMed1992

Computer-aided radiopharmaceutical design.

The ultimate goal of a QSAR analysis is prediction, which depends on the elaboration of the most appropriate set of molecular descriptors. As such, molecular description is the nucleus of QSAR and in the absence of exhaustive molecular description, rational drug design may be greatly impeded. As previously discussed, computational methods such as quantum mechanics and molecular mechanics provide molecular description at a fundamental level which then enhances the descriptive capability and predictive power of a QSAR analysis. In recognition of these capabilities, semi-empirical molecular orbital methods and molecular mechanics now have been incorporated into or interphased with QSAR programs. Such integrated packages are being successfully used in computer-aided molecular modeling. Computer-aided molecular modeling can provide the three-dimensional structure of a molecule, its chemical and physical characteristics, comparisons of structures of different molecules, and visualization of complexes formed between them. From the foregoing, predictions may be made about how related new molecules may function. Thus, the combination of quantum and/or molecular mechanics and QSAR provides a formidable weapon in the chemist's armamentarium. The molecular modeling approaches are certainly more practical to use than physicochemical methods. They also provide electronic and thermodynamic data that are not available from x-ray crystallographic data. Of course, these techniques are not confined to radiopharmaceutical development and they also could aid in the development of contrast agents for radiography or magnetic resonance imaging. We believe that as computational resources and capabilities increase over the next decade, computer-aided drug design will become a standard procedure in all drug development laboratories.

Binding Sites↗
PubMed1978

Three-dimensional molecular illustrations II: Isoelectrostatic energy contour spheres of influence applied to narcotic molecules.

A computer-generated method using quantum mechanics was applied to the calculation and subsequent plotting of nonperspective three-dimensional illustrations of molecules in vacuo. The purpose was to generate isoelectrostatic energy contour spheres for larger molecules and current drugs. The molecules chosen, morphine, meperidine, and alphaprodine, possess similar pharmacological properties. Minor configurational manipulation of meperidine and alphaprodine molecules was made to approximate the spatial configuration of the rigid morphine molecule so that direct comparisons were possible. Common areas of reactivity, potential energy minima, net atomic charges, spatial regions, and near neighbor influences are considered.

Computers↗
PubMed1986

Modeling complex molecular interactions involving proteins and DNA.

We have presented a perspective of progress in three areas of simulations of complex molecules: the development of force fields for molecular simulation; the application of computer graphics, molecular mechanics and molecular dynamics in simulations of DNA and DNA-drug complexes and the application of computer graphics, molecular mechanics and quantum mechanics in studies of enzyme substrate interactions. It is our perspective that improvements are being made in force fields, and these will allow a more accurate simulation of structures and energies of complex molecules. In the area of DNA molecular mechanics and dynamics, it is clear that the use of computer graphics model building combined with NMR NOE data is a potentially very powerful tool in accurately determining structures of drug-DNA complexes using molecular mechanics and dynamics. Finally, we are in a position to reasonably simulate structures and (qualitatively) energies for complete reaction pathways of enzymes using a combination of computer graphics, molecular mechanics and quantum mechanics. More accurate energies and pathways are sure to follow, using the combined molecular mechanics/quantum mechanics optimization developed by Singh and the free energy perturbation methods pioneered in Groningen and Houston.

Base Sequence↗
PubMed1989

Molecular electrostatic potential studies on some nitroimidazolyl and nitroheterocyclic compounds.

The electronic wave functions of 11 nitroimidazolyl and nitroheterocyclic compounds were computed using the CNDO/2 quantum chemical method. The location of the greatest nucleophilic reactivity for each molecule was predicted to be mostly near or on the nitro group. As in our previous publication (Lin Liming et al. 1985) the maximum values of the superdelocalizability index for nucleophilic reactivity S(N)max and the sum of S(N)r for each of these compounds were discovered to be significantly correlated with the radiosensitivity as indicated by log(1/C1.6), where C1.6 is the concentration of the compound required to achieve an enhancement ratio of 1.6. The electrostatic potential distribution on a plane parallel to the plane of the imidazole or heterocyclic ring was computed for these compounds with the wave functions obtained from CNDO/2 calculations. In order to analyse the steric electrostatic potential maps, the overall electrostatic potential on an imaginary surface surrounding a molecule was calculated using the multicentre multipole expansion method. It was found that a wide and deep negative potential area exists in a compound which had significant radiosensitizing efficiency, while in metronidazole, which is not an efficient radiosensitizer, the corresponding area is narrow. This phenomenon may be related to the interaction between these compounds and certain biological macromolecules. These preliminary quantum chemical results support Adams' electron affinity theory, and might be helpful in searching for new radiosensitizers.

Heterocyclic Compounds↗
PubMed2026

Electromagnetic Radiation Stimulated Learning in Perovskite Nickelates.

Biological plasticity refers to the ability of synapses to strengthen or weaken over time. These adaptive properties play a fundamental role in learning and memory, spanning many orders of magnitude in timescales. Short-term plasticity (STP) arises from rapid correlative activity, while long-term plasticity (LTP) is governed by slower biochemical processes. Here, we investigate electromagnetically driven relaxation dynamics in perovskite nickelate thin films as an analogue of biological learning behaviors. By comparing radio frequency (RF), infrared (IR), visible, and ultraviolet (UV) radiation as stimuli, we find that RF excitation primarily induces STP, while visible and IR illumination lead to reversible relaxation on behavioral timescales. In contrast, UV illumination results in persistent, non-thermal changes in conductivity over extended timescales. Notably, UV-exposed nickelate films exhibit glass-like dynamics, characterized by stretched exponential relaxation and aging phenomena. The films display habituation to repeated stimuli, along with sensitization and spontaneous recovery under controlled environments. A minimal dynamical systems model captures key qualitative features of the UV-induced resistance changes. Our results demonstrate that electromagnetic frequency enables multi-timescale relaxation spanning nearly nine orders of magnitude, suggesting perovskite nickelates as promising platforms for adaptive optoelectronic hardware and for linking computational neuroscience with emerging quantum technologies.

electromagnetic radiation↗
PubMed1989

Determination of electron density, mass density and calcium fraction by mass of soft and osseous tissues by dual energy CT.

Techniques of CT analysis of trabecular regions are concerned with bone mineral assessment, with considerable attention being paid to the effect of unknown fat content. Information concerning mass density and electron density might provide a more complete picture but is not normally obtained. A method for the calculation of mass and electron density, as well as the fraction of calcium by mass, is described and requires only a measurement of effective beam energy on the skin in addition to the CT numbers from a dual energy scan. The method uses the six major elements, H, C, N, O, P and Ca as compartments for the analysis and can also be applied to soft tissue by using only the first four. The calculated mass fraction of Ca is found to be sensitive to fat content and difference between surface and internal energies which can lead to serious underestimates below a fraction of about 0.04. Mass and electron density results are independent of fat content and only marginally affected by energy differences. Results were obtained with simple materials confirming mass density can be calculated to the order of 3% and electron density to considerably better than 1%.

Body Composition↗
PubMed1986

Computer simulations of organic reactions in solution.

Quantum and statistical mechanics have been used to determine energy profiles for the SN2 reaction of Cl- + CH3Cl in the gas phase, in aqueous solution, and in liquid DMF. The energy profile in the gas phase has the characteristic double-well form featuring unsymmetrical ion-dipole complexes as minima and a symmetrical transition state. Hydration causes the reaction surface to become almost unimodal and increases the barrier significantly. The reaction profile in DMF is intermediate between those for the gas phase and aqueous solution. The ion-dipole complexes are still free energy minima in DMF. Thus, the reaction in DMF involves initial formation of the complex before the rate-determining step. The computed results are shown to be in good accord with experimental free energies of activation. The same technique has been applied to the addition reaction of OH- + H2C = O in the gas phase and aqueous solution. Ab initio 6-31 + G* calculations indicate that the reaction proceeds essentially without activation in the gas phase. Hydration introduces a substantial energy barrier. The transition state in water has been located at a C-O separation of roughly 2 A. A key finding for both reactions is that the activation barriers induced by hydration result primarily from change in strengths rather than in numbers of solute-water hydrogen bonds along the reaction paths.

Chemical Phenomena↗
PubMed1987

A quantitative method for the detection and localization of quantum-limited events from radionuclides in cells and tissue sections by computer-enhanced video microscopy.

Cellular dynamics often involve extremely low concentrations of biologically active substances, which can be radiolabeled and detected, localized and quantitated by autoradiography. The latter may require exposures from a few days to many months. The objective of this research was to demonstrate the feasibility of reducing this long period of data collection by one to two orders of magnitude, while maintaining or improving the spatial resolution and localization in tissues and the quantitative characteristics inherent in autoradiography. A mathematical model describing the complete system was generated using energy partition calculations to estimate photon production via scintillant per H3 beta particle emission and to estimate the subsequent photon capture based upon imaging system parameters and microscope geometry. Calculations showed that, typically, a single tritium beta particle produces a maximum of 5.8 X 10(3) photons. A photon-limited camera and microscope imaging system were selected and optimized in conjunction with a specially developed physical scintillation model. Results showed that the number of detected photoevents increases monotonically with both signal integration time and, independently, with the concentration of the radionuclide. Consequently, this work demonstrates that video microscopy imaging methods can spatially and temporally quantify very low concentrations of radiolabeled substances and can reduce data acquisition times.

Beta Particles↗
PubMed2026

AI In Leukemia Diagnostics: Complementing the Pathologist's Role.

Artificial intelligence (AI) is reshaping every stage of leukemia diagnostics, from digital morphology and multiparameter flow cytometry to next-generation sequencing, multi-omics analysis, and emerging computational frontiers such as quantum-inspired feature selection. This review outlines how contemporary AI tools can automate labor-intensive quantitation, flag diagnostically salient patterns, and standardize interpretation, while the pathologist or hematologist retains authority over validation, context-specific integration, and clinical decision-making. We present an illustrative "human-in-the-loop" workflow that embeds AI modules within current laboratory information systems, emphasizing points where expert oversight mitigates algorithmic bias and resolves discordant findings. We further map the validator-integrator role across morphology, flow cytometry, and genomic/multi-omic interpretation and provide practical training competencies and use cases for AI-assisted hematopathology. Beyond technical deployment, the article addresses the educational transformation required for sustainable adoption. Drawing on international competency frameworks, including the Digital Health Competencies in Medical Education Framework and recently proposed AI-specific Entrustable Professional Activities, we map core skills that future hematopathologists must master: data-science literacy, critical appraisal of AI outputs, and ethical governance. We highlight evaluated training models such as the Pathology Informatics Essentials for Residents curriculum, Stanford Artificial Intelligence in Machine and Imaging workshops, and College of American Pathologists bootcamps and propose integration strategies adaptable across resource settings. By pairing rigorous validation with targeted education, AI can elevate rather than eclipse the diagnostic role of the leukemia specialist, enabling more timely, reproducible, and personalized patient care.

Humans↗
PubMed1989

The role of hydrated divalent metal ions in the bridging of two anionic groups. An ab initio quantum chemical and molecular mechanics study of dimethyl phosphate and formate bridged by calcium and magnesium ions.

Ab initio quantum chemical (Gaussian82) and molecular mechanics (AMBER2.0) computational techniques are employed to investigate the interaction of two anions (formate an dimethylphosphate) and a central divalent metal cation (magnesium or calcium). These systems are models for the essential GDP binding unit of the G-proteins (e.g., EF-Tu or the ras oncogene proteins) and for protein/phospholipid interactions, both of which are mediated by divalent metal cations. Various levels of hydration are utilized to examine coordination of differences between magnesium and calcium ions. Two different orientations of formate and dimethyl phosphate in direct ion contact with a magnesium ion and two waters of hydration were energy minimized with both quantum and molecular mechanics techniques. The structures and energy differences between the two orientations determined by either of the computational techniques are similar. Magnesium ion has a strong propensity to assume six coordination whereas calcium ion preferentially assumes a coordination greater than six. Likewise, water molecules attached to magnesium ion are held more rigidly than those of calcium ion, thus calcium ion is more accommodating in the exchange of water for negative ligands.

Calcium↗
PubMed1984

[Analysis of factors limiting the applications of binomial statistics in studies of mediator secretion at neuromuscular synapses].

Binomial parameters of transmitter secretion were calculated on the basis of synaptic potential analyses at frog sartorius muscle. In some synapses negative values of parameter of the p were found. These negative values often occurred at low concentrations of Ca2+ ions and small amplitude of miniature end plate potentials. The obtained data were interpreted in terms of a model which presupposes the heterogeneity of the quantum transmitter release at different sites. A computer imitation of transmitter secretion showed that the appearance of the negative p parameter values and erroneous n estimations in the experiment are related with the shape of the distribution of quantum transmitter release probability and the amplitude of miniature end plate potentials.

Animals↗
PubMed1988

Molecular modelling in design of crop protection chemicals.

Specific examples from pesticide research are given which illustrate the types of analysis employed to design optimal inhibitors for a given receptor, based on the assumption that a congeneric series of compounds behave in a related mode in the biosystem. The examples illustrate the complementary role played by computational chemistry, X-ray crystallography and computer graphics and also raise questions as to the current limitations of existing molecular mechanics and quantum mechanics techniques.

Agriculture↗