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At least 865 records · Page 48Linked to original sources
PubMed2006

Structural fluctuations and excitation transfer between adenine and 2-aminopurine in single-stranded deoxytrinucleotides.

Steady-state fluorescence measurements on the deoxytrinucleotides (5')dTp2APpA(3') and (5')dAp2APpA(3') show a temperature-dependence and a viscosity-dependence for energy transfer that qualitatively differ from those seen in our previous study of charge transfer (CT) in these systems. Time-resolved anisotropy studies and molecular dynamics simulations are presented that provide a detailed characterization of the structural dynamics of these systems and how these fluctuations modulate the electronic interaction between 2AP and its neighbors. To gain quantitative insight into the interplay of conformational fluctuations and stacking-induced energy transfer, we present results from a new hybrid quantum-classical simulation method for computing the A --> 2AP energy transfer rate that makes use of the full three-dimensional nature of the donor and acceptor transition densities. Analysis of the results shows that the standard transition dipole-transition dipole approximation for the Coulombic coupling substantially overestimates the transfer rate and that the nearest neighbor energy transfer from adenine to 2AP occurs on a much faster time scale than that for CT. This suggests that, unlike the CT dynamics where conformational "gating" plays a critical role, the large amplitude fluctuations that modulate the process are largely "frozen" out on the energy transfer time scale.

2-Aminopurine↗
PubMed2006

Fully quantum rovibrational calculation of the He(H2) bound and resonance states.

In a recent paper [J. Chem. Phys. 2005, 122, 124318], a full-dimensional quantum method, designed to efficiently compute the rovibrational states of triatomic systems with long-range interactions, was applied to the benchmark Li-(H2) ion-molecule system. The method incorporates several key features in order to accurately represent the rovibrational Hamiltonian using only modestly sized basis sets: (1) exact analytical treatment of Coriolis coupling; (2) a single bend-angle basis for all rotational states; (3) phase space optimization of the vibrational basis; (4) G(4) symmetry adaptation of the rovibrational basis. In this paper, the same methodology is applied for the first time to a van der Waals complex system, He(H2). As in the Li-(H2) study, all of the rovibrational bound states, and a number of resonance states, are computed to very high accuracy (1/10,000 of a wavenumber or better). Three different isotopologues are considered, all of which are found to have a single bound state with a very low binding energy. Several extremely long-lived Feshbach resonances are also reported.

Journal Article↗
PubMed2002

Conformational analysis of a 4-hydroxyequilenin Guanine adduct using density functional theory.

Equilenin, a component of the drug Premarin (Wyeth), can be metabolized to a quinonoid, 4-hydroxyequilenin (4-OHEN). 4-OHEN can react with 2'-deoxynucleosides to form unusual cyclic adducts, among which 4-hydroxyequilenin-2'-deoxyguanosine (4-OHEN-dG) is the major product under physiological conditions. The structure and stereochemistry of one stereoisomer, 4-OHEN-dG1, has been obtained previously using electrospray mass spectrometry and NMR methods [Shen et al. (1997) J. Am. Chem. Soc. 119, 11126-11127]; however, details of the conformations around the linkage site have not yet been investigated. The objective of this paper was to determine the conformation at the five-membered ring linkage site for this adduct. We have carried out a computational investigation involving high level quantum mechanical geometry optimization using density functional theory (DFT) for the 4-hydroxyequilenin-guanine adduct (4-OHEN-G1). Our results reveal that there are three conformational families which differ in the puckering of the five-membered ring at the linkage site and in the cyclohexene-type A ring conformation. The overall structures of all three families are "V"-shaped; however, two are quite compact while the third is more open. The lowest energy structure contains a half chair-type cyclohexene A ring, while two structures whose energies are approximately 3-4 kcal/mol higher are boat-type. Since the Watson-Crick hydrogen bonding edge of the modified guanine is obstructed by the formation of this bulky nonplanar adduct, it likely would reside in a groove of the DNA double helix.

Equilenin↗
PubMed2002

The nature and transport mechanism of hydrated hydroxide ions in aqueous solution.

Compared to other ions, protons (H(+)) and hydroxide ions (OH(-)) exhibit anomalously high mobilities in aqueous solutions. On a qualitative level, this behaviour has long been explained by 'structural diffusion' the continuous interconversion between hydration complexes driven by fluctuations in the solvation shell of the hydrated ions. Detailed investigations have led to a clear understanding of the proton transport mechanism at the molecular level. In contrast, hydroxide ion mobility in basic solutions has received far less attention, even though bases and base catalysis play important roles in many organic and biochemical reactions and in the chemical industry. The reason for this may be attributed to the century-old notion that a hydrated OH(-) can be regarded as a water molecule missing a proton, and that the transport mechanism of such a 'proton hole' can be inferred from that of an excess proton by simply reversing hydrogen bond polarities. However, recent studies have identified OH(-) hydration complexes that bear little structural similarity to proton hydration complexes. Here we report the solution structures and transport mechanisms of hydrated hydroxide, which we obtained from first-principles computer simulations that explicitly treat quantum and thermal fluctuations of all nuclei. We find that the transport mechanism, which differs significantly from the proton hole picture, involves an interplay between the previously identified hydration complexes and is strongly influenced by nuclear quantum effects.

Journal Article↗
PubMed2004

A theory of nonvertical triplet energy transfer in terms of accurate potential energy surfaces: the transfer reaction from pi,pi* triplet donors to 1,3,5,7-cyclooctatetraene.

Triplet energy transfer (TET) from aromatic donors to 1,3,5,7-cyclooctatetraene (COT) is an extreme case of "nonvertical" behavior, where the transfer rate for low-energy donors is considerably faster than that predicted for a thermally activated (Arrhenius) process. To explain the anomalous TET of COT and other molecules, a new theoretical model based on transition state theory for nonadiabatic processes is proposed here, which makes use of the adiabatic potential energy surfaces (PES) of reactants and products, as computed from high-level quantum mechanical methods, and a nonadiabatic transfer rate constant. It is shown that the rate of transfer depends on a geometrical distortion parameter gamma=(2g(2)/kappa(1))(1/2) in which g stands for the norm of the energy gradient in the PES of the acceptor triplet state and kappa(1) is a combination of vibrational force constants of the ground-state acceptor in the gradient direction. The application of the model to existing experimental data for the triplet energy transfer reaction to COT from a series of pi,pi(*) triplet donors, provides a detailed interpretation of the parameters that determine the transfer rate constant. In addition, the model shows that the observed decrease of the acceptor electronic excitation energy is due to thermal activation of C=C bond stretchings and C-C bond torsions, which collectively change the ground-state COT bent conformation (D(2d)) toward a planar triplet state (D(8h)).

Journal Article↗
PubMed2004

Experimental and theoretical study of proton spin-lattice relaxation in H2-Ar gas mixtures: critical examination of the XC(fit) potential energy surface.

Proton nuclear magnetic resonance spin-lattice relaxation time measurements have been carried out at 500 MHz proton Larmor frequency on two hydrogen-argon gas mixtures with 1.90% and 3.93% hydrogen at four different temperatures in the range 225 K < T < 337 K and at two different number densities. The results for different hydrogen mole percentages have been extrapolated to infinite dilution to obtain the contributions to the overall relaxation times arising from the hydrogen-argon interaction. The extrapolated relaxation times fall in the reciprocal regime in which relaxation times are inversely proportional to the density. Relaxation times have also been calculated using quantum mechanical close-coupled computations based on the H2-Ar XC(fit) potential energy surface obtained by Bissonnette et al. [J. Chem. Phys. 105, 2639 (1996)]. Significant differences found between the experimental and theoretical results indicate that the short-range anisotropy of the XC(fit) potential surface is too weak. The reciprocal regime is shown to have a much higher sensitivity to changes in the anisotropic component of the intermolecular potential energy surface.

Journal Article↗
PubMed2004

Modelling the propagation of terahertz radiation through a tissue simulating phantom.

Terahertz (THz) frequency radiation, 0.1 THz to 20 THz, is being investigated for biomedical imaging applications following the introduction of pulsed THz sources that produce picosecond pulses and function at room temperature. Owing to the broadband nature of the radiation, spectral and temporal information is available from radiation that has interacted with a sample; this information is exploited in the development of biomedical imaging tools and sensors. In this work, models to aid interpretation of broadband THz spectra were developed and evaluated. THz radiation lies on the boundary between regions best considered using a deterministic electromagnetic approach and those better analysed using a stochastic approach incorporating quantum mechanical effects, so two computational models to simulate the propagation of THz radiation in an absorbing medium were compared. The first was a thin film analysis and the second a stochastic Monte Carlo model. The Cole-Cole model was used to predict the variation with frequency of the physical properties of the sample and scattering was neglected. The two models were compared with measurements from a highly absorbing water-based phantom. The Monte Carlo model gave a prediction closer to experiment over 0.1 to 3 THz. Knowledge of the frequency-dependent physical properties, including the scattering characteristics, of the absorbing media is necessary. The thin film model is computationally simple to implement but is restricted by the geometry of the sample it can describe. The Monte Carlo framework, despite being initially more complex, provides greater flexibility to investigate more complicated sample geometries.

Diagnostic Imaging↗
PubMed2006

Topological quantum distillation.

We construct a class of topological quantum codes to perform quantum entanglement distillation. These codes implement the whole Clifford group of unitary operations in a fully topological manner and without selective addressing of qubits. This allows us to extend their application also to quantum teleportation, dense coding, and computation with magic states.

Journal Article↗
PubMed2004

Protein imperfections: separating intrinsic from extrinsic variation of torsion angles.

In this paper, the variation of the values of dihedral angles in proteins is divided into two categories by analyzing distributions in a database of structures determined at a resolution of 1.8 A or better [Lovell et al. (2003), Proteins Struct. Funct. Genet. 50, 437-450]. The first analysis uses the torsion angle for the Calpha-Cbeta bond (chi1) of all Gln, Glu, Arg and Lys residues ('unbranched set'). Plateaued values at low B values imply a root-mean-square deviation (RMSD) of just 9 degrees for chi1 related to intrinsic structural differences between proteins. Extrapolation to high resolution gives a value of 11 degrees , while over the entire database the RMSD is 13.4 degrees . The assumption that the deviations arise from independent intrinsic and extrinsic sources gives approximately 10 degrees as the RMSD for chi1 of these unbranched side chains arising from all disorder and error over the entire set. It is also found that the decrease in chi1 deviation that is correlated with higher resolution structures is almost entirely a consequence of the higher percentage of low-B-value side chains in those structures and furthermore that the crystal temperature at which diffraction data are collected has a negligible effect on intrinsic deviation. Those intrinsic aspects of the distributions not related to statistical or other errors, data incompleteness or disorder correlate with energies of model compounds computed with high-level quantum mechanics. Mean side-chain torsion angles for specific rotamers correlate well with local energy minima of Ace-Leu-Nme, Ace-Ile-Nme and Ace-Met-Nme. Intrinsic RMSD values in examples with B < or = 20 A2 correlate inversely with calculated values for the relevant rotational energy barriers: from a low of 6.5 degrees for chi1 of some rotamers of Ile to a high of 14 degrees for some Met chi3 for fully tetrahedral angles and much higher for chi angles around bonds that are tetrahedral at one end and planar at the other (e.g. 30 degrees for chi2 of the gauche- rotamer of Phe). For the lower barrier Met chi3 rotations there are relatively more well validated cases near eclipsed values and calculated torques from the rest of the protein structure either confine or force the Cepsilon atom into the strained position. These results can be used to evaluate the variability and accuracy of chi angles in crystal structures and also to decide whether to restrain side-chain angles in refinement as a function of the resolution and atomic B values, depending on whether one aims for a realistic distribution of values or a spread that is statistically suitable to the probable data-set errors.

Carbon↗
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↗
PubMed2005

Computing kinetic isotope effects for chorismate mutase with high accuracy. A new DFT/MM strategy.

A novel procedure has been applied to compute experimentally unobserved intrinsic kinetic isotope effects upon the rearrangement of chorismate to prephenate catalyzed by B. subtilis chorismate mutase. In this modified QM/MM approach, the "low-level" QM description of the quantum region is corrected during the optimization procedure by means of a "high-level" calculation in vacuo, keeping the QM-MM interaction contribution at a quantum "low-level". This allows computation of energies, gradients, and Hessians including the polarization of the QM subsystem and its interaction with the MM environment, both terms calculated using the low-level method at a reasonable computational cost. New information on an important enzymatic transformation is provided with greater reliability than has previously been possible. The predicted kinetic isotope effects on Vmax/Km are 1.33 and 0.86 (at 30 degrees C) for 5-3H and 9-3H2 substitutions, respectively, and 1.011 and 1.055 (at 22 degrees C) for 1-13C and 7-18O substitutions, respectively.

Chorismate Mutase↗
PubMed2000

Computer simulation of primary kinetic isotope effects in the proposed rate-limiting step of the glyoxalase I catalyzed reaction.

The proposed rate-limiting step of the glyoxalase I catalyzed reaction is the proton abstraction from the C1 carbon of the substrate by Glu(172). Here we examine primary kinetic isotope effects and the influence of quantum dynamics on this process by computer simulations. The calculations utilize the empirical valence bond method in combination with the molecular dynamics free energy perturbation technique and path integral simulations. For the enzyme-catalyzed reaction a H/D kinetic isotope effect of 5.0 +/- 1. 3 is predicted in reasonable agreement with the experimental result of about 3. Furthermore, the magnitude of quantum mechanical effects is found to be very similar for the enzyme reaction and the corresponding uncatalyzed process in solution, in agreement with other studies. The problems associated with attaining the required accuracy in order for the present approach to be useful as a diagnostic tool for the study of enzyme reactions are also discussed.

Catalysis↗
PubMed2003

Determining the strengths of hydrogen bonds in solid-state ammonia and urea: insight from periodic DFT calculations.

Plane-wave density functional theory has been applied to determine the strengths of hydrogen bonds in the phase I crystal structures of ammonia and urea. For ammonia, each component of the trifurcated hydrogen bond has been found to be almost as strong as a standard N-H.N interaction, and for urea the strengths of the two different N-H.O interactions have been determined by a quantum mechanical technique for the first time.

Ammonia↗
PubMedDate not supplied

A comparative study of isodensity surfaces using ab initio and ASA density functions.

In this article, we report a visual comparison between several of the available methods for constructing electronic density functions. The density forms studied include ab initio, atomic shell approximation, and promolecular densities. A graphical comparison is made for six different molecules at different levels of density function values. The differences between the various density functions are analysed by considering a molecular quantum self-similarity measure and the required computational time for all molecules at all computation levels is considered.

Algorithms↗
PubMed2004

NMR and inelastic incoherent neutron scattering (IINS) studies of monohydroxy-17 and -21-substituted derivatives of progesterone.

Internal dynamics of 17- and 21-substituted progesterone derivatives was studied by the methods NMR, inelastic incoherent neutron scattering (IINS) and quantum chemical calculations. Comparison of the computer simulation of the phonon density of states (PDS) spectrum performed by the density functional theory (DFT) method with the spectrum obtained after a transformation of the experimental results permits an interpretation of subsequent modes. Only for 17OH prg the second moment of NMR line decreases to 10 G2 near room temperature, most probably because of the oscillations about direction of inter-molecular hydrogen bond. Significant mobility of protons in this compound is also confirmed by a low intensity of the elastic peak in INS and broadening of this spectrum.

Computer Simulation↗
PubMed2006

Beyond vinyl: electronic structure of unsaturated propen-1-yl, propen-2-yl, 1-buten-2-yl, and trans-2-buten-2-yl hydrocarbon radicals.

Vertical excitation energies and oscillator strengths for several valence and Rydberg electronic states of vinyl, propen-1-yl, propen-2-yl, 1-buten-2-yl, and trans-2-buten-2-yl radicals are calculated using the equation-of-motion coupled cluster methods with single and double substitutions (EOM-CCSD). The ground and the lowest excited state (n <-- pi) equilibrium geometries are calculated using the CCSD(T) and EOM-SF-CCSD methods, respectively, and adiabatic excitation energies for the n <-- pi state are reported. Systematic changes in the geometries, excitation energies, and Rydberg state quantum defects within this group of radicals are discussed.

Alkenes↗
PubMed1993

Strategies for indirect computer-aided drug design.

This review is intended to describe some of the methods and procedures used for computer-aided drug design when the structure of the macromolecular target is unknown, as is the case for CNS active drugs. Strategies and methods used in computer-aided design of drugs in such instances must be "indirect," i.e., focusing on the characterization of the ligands themselves. This situation is different from one in which the three-dimensional structure of the macromolecular target for a drug is known, for example, for drugs that are enzyme inhibitors, allowing "direct" characterization of ligand-receptor interactions. Two qualitatively different "indirect" approaches are described here. One, called 2D-QSAR, is briefly reviewed. It is based on delineating regression relationships between a specified biological end point and properties of the compounds eliciting it. The other, based on pharmacophore development, constitutes the main part of this review. Several levels of pharmacophore development are described, which differ in the extent to which they encompass fundamental molecular properties that are determinants of receptor recognition and activation. The strengths and limitations of each procedure are discussed and illustrated by examples. Two methods for obtaining model receptor structures are then briefly described. Both rely on the prior success of the indirect methods in obtaining ligand properties that modulate receptor recognition and activation. These emerging capabilities have the potential to bridge the gap between indirect and direct methods of drug design, since, if successful, the design process can continue in a direct mode using explicit characterization of drug-receptor interactions. Strategies for hypothesis validation and use of hypothesis for drug design and discovery are also briefly reviewed. The final sections of this review describe specific computational tools such as molecular mechanics and quantum mechanical methods used to characterize and identify relevant molecular properties and indicate some areas for future development of computational chemistry methods that could increase its effectiveness in the design of novel drugs.

Computer Simulation↗
PubMed2006

Computational photochemistry of retinal proteins.

High spectral tunability and quantum yield are the striking features of rhodopsin photochemistry. They rely on a strong and complex interaction of their chromophore, the protonated Schiff base of retinal, with its protein environment. In this article, we review the progress in the computational modeling of these systems, focusing on the optical properties and the excited state dynamics. While the earlier success of atomistic theoretical models was based on the breakthrough in X-ray crystallography and combined quantum mechanical molecular mechanical (QM/MM) methodology, recent advances point out the importance of high-level QM methods and the incorporation of effects that are neglected in conventional QM/MM or ONIOM schemes, like polarization and charge transfer.

Computational Biology↗