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PubMed2003

Optical spectroscopic investigations of model beta-sheet hairpins in aqueous solution.

In this contribution we report optical spectroscopic data on a series of designed beta hairpins previously shown by NMR to contain a substantial population of beta-sheet structure. These models contain a designed hydrophobic cluster and a (D)Pro-Gly sequence to promote formation of a turn geometry. FTIR, electronic and vibrational CD (ECD and VCD) spectra for these small peptides are comparable to expected bandshapes for peptides of high beta-sheet content. The (D)Pro-Gly sequence provides a better turn motif than Asn-Gly as measured by its beta-sheet spectral characteristics. IR and VCD spectra are in qualitative agreement with theoretical simulations based on transfer of parameters from ab initio quantum mechanical force field and intensity computations for the turn and strands. These calculations provide assignments for some distinguishing modes in both IR and VCD spectra. Increased sheet structure can be induced in these hairpins by use of mixed solvent conditions. Thermal denaturation studies reveal that these hairpins undergo very broad unfolding transitions. Guanidine hydrochloride unfolding transitions for the selected hairpin models are similarly broad. However, the "end-states" of temperature and chaotropic denaturation are spectroscopically differentiable.

Circular Dichroism↗
PubMed2002

Descriptors, physical properties, and drug-likeness.

We have investigated techniques for distinguishing between drugs and nondrugs using a set of molecular descriptors derived from semiempirical molecular orbital (AM1) calculations. The "drug" data set of 2105 compounds was derived from the World Drug Index (WDI) using a procedure designed to select real drugs. The "nondrug" data set was the Maybridge database. We have first investigated the dimensionality of physical properties space based on a set of 26 descriptors that we have used successfully to build absorption, distribution, metabolism, and excretion-related quantitative structure-property relationship models. We discuss the general nature of the descriptors for physical property space and the ability of these descriptors to distinguish between drugs and nondrugs. The third most significant principal component of this set of descriptors serves as a useful numerical index of drug-likeness, but no others are able to distinguish between drugs and nondrugs. We have therefore extended our set of descriptors to a total of 66 and have used recursive partitioning to identify the descriptors that can distinguish between drugs and nondrugs. This procedure pointed to two of the descriptors that play an important role in the principal component found above and one more from the set of 40 extra descriptors. These three descriptors were then used to train a Kohonen artificial neural net for the entire Maybridge data set. Projecting the drug database onto the map obtained resulted in a clear distinction not only between drugs and nondrugs but also, for instance, between hormones and other drugs. Projection of 42 131 compounds from the WDI onto the Kohonen map also revealed pronounced clustering in the regions of the map assigned as druglike.

Chemical Phenomena↗
PubMed1995

Synthesis and characterization of adducts of alachlor and 2-chloro-N-(2,6-diethylphenyl)acetamide with 2'-deoxyguanosine, thymidine, and their 3'-monophosphates.

Adducts of the preemergence herbicide 2-chloro-N-(methoxymethyl)-N-(2,6-diethylphenyl)-acetamide (alachlor) and 2-chloro-N-(2,6-diethylphenyl)acetamide (CDEPA) with 2'-deoxyguanosine, thymidine, 2'-deoxyguanosine 3'-monophosphate, and thymidine 3'-monophosphate have been synthesized and characterized. Under mildly basic conditions alachlor and CDEPA form N-1 adducts with 2'-deoxyguanosine and N-3 adducts with thymidine as a result of chlorine displacement. In addition, alachlor formed an N-7 adduct with 2'-deoxyguanosine, 7-[[(N-(methoxymethyl)-N-(2,6-diethylphenyl)carbamoyl]methyl]guani ne. N-1 adducts of alachlor and CDEPA with 2'-deoxyguanosine 3'-monophosphate and N-3 adducts with thymidine 3'-monophosphate are also described. In addition to spectroscopic data, structural proof included the dephosphorylation of each nucleotide adduct to its corresponding nucleoside adduct by nuclease P1. Alachlor and alachlor adducts but not CDEPA and CDEPA adducts exhibited rotational isomerism as evidenced by proton and 13C NMR studies. These rotamers were attributed to hindered rotation about the shortened N-carbonyl bond. Computational methods employing molecular mechanics and quantum mechanics were used to characterize the structures and energies of these rotamers to account for the patterns of duplicate NMR resonances observed.

Acetamides↗
PubMed2003

Electrochemical potentials and pressures of biofluids from common experimental data.

Many biosystems are complex mixtures of disparate biofluids. To study contact and transport phenomena in these mixtures, one has to apply much information on the biofluids which are components of the mixtures. A lot of the corresponding data can be extracted by means of experiments. However, it is not always easy to obtain experimental results on rather deep physical characteristics of biofluids, especially if the bioparticles are complicated systems and the fluid coexists in the mixture with a large number of other fluids. In these cases, the necessary data can, in principle, be extracted from those results which are easier to obtain experimentally. The present work proposes a method to evaluate the biofluid equilibrium pressure and electrochemical potential from common experimental values of the fluid concentration and absolute temperature as well as the fluid-particle mass, volume and spin. In so doing, the nonzero values of the particle volume are accounted for. The procedure is illustrated with a numerical example on the fluid of red blood cells (or erythrocytes) in human blood. The pressure values obtained are 49.1 and 38.8 micropascals for men and women respectively whereas the electrochemical-potential values are -2.124 and -2.130 electronvolts for men and women respectively.

Body Fluids↗
PubMed2004

Quantitative structure-activity relationships from optimised ab initio bond lengths: steroid binding affinity and antibacterial activity of nitrofuran derivatives.

The present day abundance of cheap computing power enables the use of quantum chemical ab initio data in Quantitative Structure-Activity Relationships (QSARs). Optimised bond lengths are a new such class of descriptors, which we have successfully used previously in representing electronic effects in medicinal and ecological QSARs (enzyme inhibitory activity, hydrolysis rate constants and pKas). Here we use AM1 and HF/3-21G* bond lengths in conjunction with Partial Least Squares (PLS) and a Genetic Algorithm (GA) to predict the Corticosteroid-Binding Globulin (CBG) binding activity of the classic steroid data set, and the antibacterial activity of nitrofuran derivatives. The current procedure, which does not require molecular alignment, produces good r2 and q2 values. Moreover, it highlights regions in the common steroid skeleton deemed relevant to the active regions of the steroids and nitrofuran derivatives.

Adrenal Cortex Hormones↗
PubMed2000

Entropy computing via integration over fractal measures.

We discuss the properties of invariant measures corresponding to iterated function systems (IFSs) with place-dependent probabilities and compute their Renyi entropies, generalized dimensions, and multifractal spectra. It is shown that with certain dynamical systems, one can associate the corresponding IFSs in such a way that their generalized entropies are equal. This provides a new method of computing entropy for some classical and quantum dynamical systems. Numerical techniques are based on integration over the fractal measures. (c) 2000 American Institute of Physics.

Journal Article↗
PubMed2000

Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities.

The alanine helix provides a model system for studying the energetics of interaction between water and the helical peptide group, a possible major factor in the energetics of protein folding. Helix formation is enthalpy-driven (-1.0 kcal/mol per residue). Experimental transfer data (vapor phase to aqueous) for amides give the enthalpy of interaction with water of the amide group as approximately -11.5 kcal/mol. The enthalpy of the helical peptide hydrogen bond, computed for the gas phase by quantum mechanics, is -4.9 kcal/mol. These numbers give an enthalpy deficit for helix formation of -7.6 kcal/mol. To study this problem, we calculate the electrostatic solvation free energy (ESF) of the peptide groups in the helical and beta-strand conformations, by using the delphi program and parse parameter set. Experimental data show that the ESF values of amides are almost entirely enthalpic. Two key results are: in the beta-strand conformation, the ESF value of an interior alanine peptide group is -7.9 kcal/mol, substantially less than that of N-methylacetamide (-12.2 kcal/mol), and the helical peptide group is solvated with an ESF of -2.5 kcal/mol. These results reduce the enthalpy deficit to -1.5 kcal/mol, and desolvation of peptide groups through partial burial in the random coil may account for the remainder. Mutant peptides in the helical conformation show ESF differences among nonpolar amino acids that are comparable to observed helix propensity differences, but the ESF differences in the random coil conformation still must be subtracted.

Alanine↗
PubMed2003

Tuning heme redox potentials in the cytochrome C subunit of photosynthetic reaction centers.

The photosynthetic reaction center (RC) from Rhodopseudomonas viridis contains four cytochrome c hemes. They establish the initial part of the electron transfer (ET) chain through the RC. Despite their chemical identity, their midpoint potentials cover an interval of 440 mV. The individual heme midpoint potentials determine the ET kinetics and are therefore tuned by specific interactions with the protein environment. Here, we use an electrostatic approach based on the solution of the linearized Poisson-Boltzmann equation to evaluate the determinants of individual heme redox potentials. Our calculated redox potentials agree within 25 meV with the experimentally measured values. The heme redox potentials are mainly governed by solvent accessibility of the hemes and propionic acids, by neutralization of the negative charges at the propionates through either protonation or formation of salt bridges, by interactions with other hemes, and to a lesser extent, with other titratable protein side chains. In contrast to earlier computations on this system, we used quantum chemically derived atomic charges, considered an equilibrium-distributed protonation pattern, and accounted for interdependencies of site-site interactions. We provide values for the working potentials of all hemes as a function of the solution redox potential, which are crucial for calculations of ET rates. We identify residues whose site-directed mutation might significantly influence ET processes in the cytochrome c part of the RC. Redox potentials measured on a previously generated mutant could be reproduced by calculations based on a model structure of the mutant generated from the wild type RC.

Binding Sites↗
PubMed2000

Decay and slowing down of the multiquanta Davydov-like solitons in molecular chains.

Dynamics and the stability of the multivibron solitons in molecular chains have been examined by means of the perturbation method based upon the inverse scattering transform. We demonstrate that due to the coupling with phonons the soliton radiates energy which causes its slowing down and gradual decay of its amplitude. It was shown that the soliton lifetime depends strongly on temperature and the values of the basic physical parameters of the system. On the basis of these results the possible role of the multivibron solitons in the intramolecular vibrational energy transfer has been critically assessed.

Energy Transfer↗
PubMed2000

Minimization methods for the one-particle dirac equation.

Taking into account relativistic effects in quantum chemistry is crucial for accurate computations involving heavy atoms. Standard numerical methods can deal with the problem of variational collapse and the appearance of spurious roots only in special cases. The goal of this Letter is to provide a general and robust method to compute particle bound states of the Dirac equation.

Journal Article↗
PubMed2003

Equilibrium model of bimodal distributions of epitaxial island growth.

We present a nanostructure diagram for use in designing heteroepitaxial systems of quantum dots. The nanostructure diagram is computed using a new equilibrium statistical physics model and predicts the island size and shape distributions for a range of combinations of growth temperature and amount of deposited material. The model is applied to Ge on Si(001), the archetype for bimodal island growth, and the results compare well with data from atomic force microscopy of Ge/Si islands grown by chemical vapor deposition.

Journal Article↗
PubMed1992

Dynamic control of inositol 1,4,5-trisphosphate-induced Ca2+ release: a theoretical explanation for the quantal release of Ca2+.

A theoretical model has been elaborated in order to describe the kinetics of Ca2+ release induced by inositol 1,4,5-trisphosphate (IP3). The model is based on the existence of a key molecule that controls the interconversion of open and closed forms of the Ca2+ channel. The model can quantitatively explain the previously obtained experimental observations that showed that a continuous IP3 stimulus leads to a biphasic Ca2+ release and that successive IP3 additions provoke repetitive bursts of Ca2+ release. Other published interpretations of these observations are discussed.

Calcium↗
PubMed2004

Fractionation of peptide with disulfide bond for quantum mechanical calculation of interaction energy with molecules.

We present a computational study of a recently developed molecular fractionation with conjugated caps (MFCC) method for application to peptide/protein that has disulfide bonds. Specifically, we employ the MFCC approach to generate peptide fragments in which a disulfide bond is cut and a pair of conjugated caps are inserted. The method is tested on two peptides interacting with a water molecule. The first is a dipeptide consisting of two cysteines (Cys-Cys) connected by a disulfide bond and the second is a seven amino acid peptide consisting of Gly-Cys-Gly-Gly-Gly-Cys-Gly with a disulfide cross link. One-dimensional peptide-water potential curves are computed using the MFCC method at various ab initio levels for a number of interaction geometries. The calculated interaction energies are found to be in excellent agreement with the results obtained from the corresponding full system ab initio calculations for both peptide/water systems. The current study provides further numerical support for the accuracy of the MFCC method in full quantum mechanical calculation of protein/peptide that contains disulfide bonds.

Binding Sites↗
PubMed1993

Theoretical conformational analyses of endothelin-1 in vacuum, aqueous, and lipid environments.

Endothelin-1 (ET-1) is a flexible molecule capable of existing in multiple shapes (conformations) depending on the surrounding molecular solvation. The conformational diversity of ET-1 was studied in three solvation spheres (gas phase, aqueous, and membrane lipid) with the new evolving biotechnology of computational biomolecular simulation. Simulations were performed using a combination of molecular mechanics, molecular dynamics, and semiempirical quantum mechanics calculations in a RISC architecture large-scale computing environment. Marked differences between the gas phase "folded" conformation and the membrane lipid "extended" conformation were identified.

Chemical Phenomena↗
PubMed2003

Substituting a qubit for an arbitrarily large number of classical bits.

We show that a qubit can be used to substitute for a classical analog system requiring an arbitrarily large number of classical bits to represent digitally. Let a physical system S interact locally with a classical field varphi(x) as S travels directly from point A to point B. Our task is to use S to answer a simple yes/no question about varphi(x). If S is a qubit, the task can be done perfectly. We show that any classical system S must encode an arbitrarily large number of classical bits to solve the same task. This result implies a large quantum advantage in the memory size necessary for some computations. We also show that no finite amount of one-way classical communication can perfectly simulate the effect of quantum entanglement.

Journal Article↗
PubMed2001

Quantum chemical modeling of Co--C bond activation in B(12)-dependent enzymes.

Recent progress in computational modeling of the catalytic activation of cobalt-carbon bond cleavage shows that quantum chemical calculations could be an important part of coenzyme B(12) research. Particular emphasis has been placed on density functional theory, which is now emerging as a powerful tool to elucidate the electronic structure and spectroscopic properties of the active sites of metalloenzymes.

Cobalt↗
PubMed1999

Quality of preimplant low-dose tomography.

OBJECTIVES: The aim of this study was to test the influence of radiation dose on image quality in mandibular preimplant computed tomographic examinations and to compare the quality of computed and conventional spiral tomographic images. STUDY DESIGN: Cross-sectional images were obtained on 17 patients with conventional spiral tomography (Scanora technique) and reformatted computed tomography at 40 and 80 mAs. Observers graded the acceptability of images for implant planning and traced the contour of the mandibular body and canal. RESULTS: Conventional spiral tomographic images scored significantly higher than computed tomographic images whereas mean score differences between computed tomographic techniques were not statistically significant. Anatomic structures, in particular the mandibular canal, were more frequently untraceable in high-dose than in low-dose computed tomography but always traceable in conventional tomograms. CONCLUSION: Conventional spiral tomograms were subjectively preferred over computed tomographic images. For mandibular implant planning, computed tomography examinations can be performed with lower-than-standard mAs. Quantum noise seems to contribute to the visibility of anatomic structures in reformatted computed tomographic images.

Adult↗
PubMed2000

Ultimate physical limits to computation

Computers are physical systems: the laws of physics dictate what they can and cannot do. In particular, the speed with which a physical device can process information is limited by its energy and the amount of information that it can process is limited by the number of degrees of freedom it possesses. Here I explore the physical limits of computation as determined by the speed of light c, the quantum scale h and the gravitational constant G. As an example, I put quantitative bounds to the computational power of an 'ultimate laptop' with a mass of one kilogram confined to a volume of one litre.

Journal Article↗