Molecular orbital studies on lipids: conformation of glycerol trivalerate by the PCILO method.
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Computers↗
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Electrode potentials for bioreductive agents from neural networks.
The one-electron electrode potentials at pH 7 have been predicted to an average accuracy of about 70 mV for a number of nitrobenzenes, nitrofurans and nitroimidazoles using a neural network. The inputs were the heat of formation and the free energy of hydration of both the nitroarene and its radical anion. The heats of formation were calculated using semiempirical molecular orbital methods; the free energies of hydration were calculated using a modified Born equation with additional semiempirical terms. Since these inputs can be calculated quickly, the neural network promises to be very useful in the design of molecules such as bioreductive agents where the electrode potential is of crucial importance. The success of the neural network in this problem implies that the errors, primarily in the semiempirical heat of formation, are systematic, and offers the hope that these may be corrected in future generations of the semiempirical methods.
Antineoplastic Agents↗
Prediction of the reactivities of cyclopenta-polynuclear aromatic hydrocarbons by quantum mechanical methods.
1. The direction of epoxide ring opening may be predicted using the techniques of theoretical chemistry by comparing the computed total energy of the two possible carbocations formed. 2. To predict the direction of epoxide ring opening and the potential binding of aceanthrylene 1,2-epoxide to biopolymers, quantum mechanical calculations were performed on the two potential hydroxy carbocations. 3. The 2-hydroxy carbocation (II) was favoured over the 1-hydroxy carbocation by 11.8 kcal/mol. Molecule II had more positive charge at the meso carbon group than at the nominally charged 1 position. Both the lowest unoccupied molecular orbital and the molecular electrostatic potential confirm this result, and indicate the possibility of unusual adducts to biopolymers. 4. Similar calculations on the equivalent epoxides of acenaphthylene and acephenanthrylene do not show the same results. 5. Modelling the addition products of II with small nucleophiles indicates that these unusual addition products do not form, and that the interaction is controlled by electronic effects and not electrostatic effects. 6. The calculations on acephenanthrylene demonstrate the importance of including the hydroxyl group when making predictions relative to epoxide ring opening. 7. Molecular descriptors are surrogates for the interaction of that molecule with an often unknown biological target. In cases where molecular descriptors are used without information about the target, small quantitative differences may not be appropriate discriminators.
Chemical Phenomena↗
A quantum accounting and detective quantum efficiency analysis for video-based portal imaging.
The quality of images generated with radiographic imaging systems can be degraded if an inadequate number of secondary quanta are used at any stage before production of the final image. A theoretical technique known as a "quantum accounting diagram" (QAD) analysis has been developed recently to predict the detective quantum efficiency (DQE) of an imaging system as a function of spatial frequency based on an analysis of the propagation of quanta. It is used to determine the "quantum sink" stage(s) (stages which degrade the DQE of an imaging system due to quantum noise caused by a finite number of quanta), and to suggest design improvements to maximize image quality. We have used this QAD analysis to evaluate a video-based portal imaging system to determine where changes in design will have the most benefit. The system consists of a thick phosphor layer bonded to a 1 mm thick copper plate which is viewed by a T.V. camera. The imaging system has been modeled as ten cascaded stages, including: (i) conversion of x-ray quanta to light quanta; (ii) collection of light by a lens; (iii) detection of light quanta by a T.V. camera; (iv) the various blurring processes involved with each component of the imaging system; and, (v) addition of noise from the T.V. camera. The theoretical DQE obtained with the QAD analysis is in excellent agreement with the experimental DQE determined from previously published data. It is shown that the DQE is degraded at low spatial frequencies (< 0.25 cycles/mm) by quantum sinks both in the number of detected x rays and the number of detected optical quanta. At higher spatial frequencies, the optical quantum sink becomes the limiting factor in image quality. The secondary quantum sinks can be prevented, up to a spatial frequency of 0.5 cycles/mm, by increasing the overall system gain by a factor of 9 or more, or by improving the modulation transfer function (MTF) of components in the optical chain.
Biophysical Phenomena↗
Intermolecular double-quantum coherence MR microimaging of pig tail with unique image contrast.
Image contrast in intermolecular double-quantum coherence (iDQC) imaging of a pig tail was investigated on a 7.05-T microimaging scanner. In addition to TR (repetition time) and TE (echo time), the time interval tau between radio frequency pulses during iDQC evolution and the areas under the iDQC-encode gradients in the iDQC imaging sequence were also used to manipulate image contrast. When suitable imaging parameters were selected, images with unique contrast, such as those with certain regions of the sample highlighted, were obtained without using contrast agents. The effects of iDQC-encode gradient on image contrast were studied quantitatively, and the unique contrast imposed by the related diffusion weighting was also shown. Experimental results demonstrated that the iDQC images have contrast fundamentally different from the conventional single-quantum coherence images.
Animals↗
Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase.
Elucidating the role of nuclear quantum mechanical (NQM) effects in enzyme catalysis is a topic of significant current interest. Despite the great experimental progress in this field it is important to have theoretical approaches capable of evaluating and analyzing nuclear quantum mechanical contributions to catalysis. In this study, we use the catalytic reaction of lipoxygenase, which is characterized by an extremely large kinetic isotope effect, as a challenging test case for our simulation approach. This is done by applying the quantum classical path (QCP) method with an empirical valence bond potential energy surface. Our computational strategy evaluates the relevant NQM corrections and reproduces the large observed kinetic isotope effect and the temperature dependence of the H atom transfer reaction while being less successful with the D atom transfer reaction. However, the main point of our study is not so much to explore the temperature dependence of the isotope effect but rather to develop and validate an approach for calculations of nuclear quantum mechanical contributions to activation free energies. Here, we find that the deviation between the calculated and observed activation free energies is small for both H and D at all investigated temperatures. The present study also explores the nature of the reorganization energy in the enzyme and solution reactions. It is found that the outer-sphere reorganization energy is extremely small. This reflects the fact that the considered reaction involves a very small charge transfer. The implication of this finding is discussed in the framework of the qualitative vibronic model. The main point of the present study is, however, that the rigorous QCP approach provides a reliable computational tool for evaluating NQM contributions to catalysis even when the given reaction includes large tunneling contributions. Interestingly, our results indicate that the NQM effects in the lipoxygenase reaction are similar in the enzyme and in the reference solution reactions, and thus do not contribute to catalysis. We also reached similar conclusions in studies of other enzymes.
Computer Simulation↗
High performance computing in biology: multimillion atom simulations of nanoscale systems.
Computational methods have been used in biology for sequence analysis (bioinformatics), all-atom simulation (molecular dynamics and quantum calculations), and more recently for modeling biological networks (systems biology). Of these three techniques, all-atom simulation is currently the most computationally demanding, in terms of compute load, communication speed, and memory load. Breakthroughs in electrostatic force calculation and dynamic load balancing have enabled molecular dynamics simulations of large biomolecular complexes. Here, we report simulation results for the ribosome, using approximately 2.64 million atoms, the largest all-atom biomolecular simulation published to date. Several other nano-scale systems with different numbers of atoms were studied to measure the performance of the NAMD molecular dynamics simulation program on the Los Alamos National Laboratory Q Machine. We demonstrate that multimillion atom systems represent a 'sweet spot' for the NAMD code on large supercomputers. NAMD displays an unprecedented 85% parallel scaling efficiency for the ribosome system on 1024 CPUs. We also review recent targeted molecular dynamics simulations of the ribosome that prove useful for studying conformational changes of this large biomolecular complex in atomic detail.
Computational Biology↗
Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution.
We describe the implementation of an adaptive umbrella sampling method, making use of the weighted histogram analysis method, for computing multidimensional potential of mean force for chemical reaction in solution. The approach is illustrated by investigating the effect of aqueous solution on the free energy surface for the proton transfer reaction of [H(3)N-H-NH(3)](+) using a combined quantum mechanical and molecular mechanical AM1/TIP3P potential.
Mathematical Computing↗
Peptide models. XXXIII. Extrapolation of low-level Hartree-Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory.
At the dawn of the new millenium, new concepts are required for a more profound understanding of protein structures. Together with NMR and X-ray-based 3D-structure determinations in silico methods are now widely accepted. Homology-based modeling studies, molecular dynamics methods, and quantum mechanical approaches are more commonly used. Despite the steady and exponential increase in computational power, high level ab initio methods will not be in common use for studying the structure and dynamics of large peptides and proteins in the near future. We are presenting here a novel approach, in which low- and medium-level ab initio energy results are scaled, thus extrapolating to a higher level of information. This scaling is of special significance, because we observed previously on molecular properties such as energy, chemical shielding data, etc., determined at a higher theoretical level, do correlate better with experimental data, than those originating from lower theoretical treatments. The Ramachandran surface of an alanine dipeptide now determined at six different levels of theory [RHF and B3LYP 3-21G, 6-31+G(d) and 6-311++G(d,p)] serves as a suitable test. Minima, first-order critical points and partially optimized structures, determined at different levels of theory (SCF, DFT), were completed with high level energy calculations such as MP2, MP4D, and CCSD(T). For the first time three different CCSD(T) sets of energies were determined for all stable B3LYP/6-311++G(d,p) minima of an alanine dipeptide. From the simplest ab initio data (e.g., RHF/3-21G) to more complex results [CCSD(T)/6-311+G(d,p)//B3LYP/6-311++G(d,p)] all data sets were compared, analyzed in a comprehensive manner, and evaluated by means of statistics.
Alanine↗
Simple linear QSAR models based on quantum similarity measures.
A novel QSAR approach based on quantum similarity measures was developed and tested in this paper. This approach consists of replacing the usual physicochemical parameters employed in QSAR analysis, such as octanol-water partition coefficient or Hammett sigma constant, by appropriate quantum chemical descriptors. The methodological basis for this substitution is found in recent theoretical studies [J. Comput. Chem. 1998, 19, 1575-1583, J. Comput. -Aided Mol. Des. 1999, 13, 259-270], in which it was demonstrated that both molecular hydrophobic character and electronic substituent effect can be modeled by appropriately chosen quantum self-similarity measures (QS-SM). The most important aim of this study was to prove that selected QS-SM descriptors can be advantageously used in empirical QSAR analysis instead of classical descriptors. For this purpose several QSAR correlations are proposed, in which empirical descriptors such as Hammett sigma constants or log P values are replaced by the appropriate QS-SM. These examples involve: (i) a set of benzenesulfonamides which bind to human carbonic anhydrase, (ii) a set of benzylamines as competitive inhibitors of the enzyme trypsin, and (iii) a set of indole derivatives which are benzodiazepine receptor inverse agonist site ligands. Simple linear QSAR models were developed in order to obtain mathematical relationships between the biological activity and the pertinent quantum chemical descriptors. The validity of the obtained QSAR models is supported by comparison of the observed and predicted values of the biological activity and by a statistical analysis based on a randomization test.
Benzylamines↗
Potential energy functions for atomic-level simulations of water and organic and biomolecular systems.
An overview is provided on the development and status of potential energy functions that are used in atomic-level statistical mechanics and molecular dynamics simulations of water and of organic and biomolecular systems. Some topics that are considered are the form of force fields, their parameterization and performance, simulations of organic liquids, computation of free energies of hydration, universal extension for organic molecules, and choice of atomic charges. The discussion of water models covers some history, performance issues, and special topics such as nuclear quantum effects.
Biophysics↗
A comparative theoretical study of dipeptide solvation in water.
Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine-alanine in water, with focus on the solvation and electrostatic properties using a range of theoretical methods, from purely classical force fields, through mixed quantum mechanical/molecular mechanical simulations, to fully quantum mechanical Car-Parrinello calculations. The results of these studies show that the solvation pattern is similar for all methods used for most atoms in the dipeptide, but can differ substantially for some groups; namely the carboxy and aminoterminii, and the backbone amid NH group. This might have implications in other theoretical studies of peptides and proteins with charged -NH(3) (+) and -CO(2) (-) side chains solvated in water. Hybrid quantum mechanical/molecular mechanical simulations successfully reproduce the solvation patterns from the fully quantum mechanical simulations (PACS numbers: 87.14.Ee, 87.15.Aa, 87.15.He, 71.15.Pd).
Alanine↗
Anesthesia, consciousness and hydrophobic pockets--a unitary quantum hypothesis of anesthetic action.
1. A consensus view holds that anesthetics act by van der Waals forces in hydrophobic pockets of select brain proteins to ablate consciousness. 2. What is consciousness? Enigmatic features of consciousness (e.g. 'qualia', binding, non-computability, pre-conscious-->conscious transition, nondeterministic free will) may be explained by the occurrence of quantum coherent states in the brain. 3. Van der Waals electron pair couplings (London forces) in hydrophobic pockets in non-anesthetic (conscious) conditions are a particular type of quantum capable of supporting macroscopic quantum coherence. 4. The mechanism of anesthetics may be to inhibit electron mobility and London forces necessary for quantum states and consciousness in hydrophobic pockets of select brain proteins.
Anesthesia↗
Quantum technology: the second quantum revolution.
We are currently in the midst of a second quantum revolution. The first quantum revolution gave us new rules that govern physical reality. The second quantum revolution will take these rules and use them to develop new technologies. In this review we discuss the principles upon which quantum technology is based and the tools required to develop it. We discuss a number of examples of research programs that could deliver quantum technologies in coming decades including: quantum information technology, quantum electromechanical systems, coherent quantum electronics, quantum optics and coherent matter technology.
Computing Methodologies↗
Computational engineering of metallic nanostructures and nanomachines.
Small structures with dimensions in the nanometer regime play an important role within a lot of modern technological branches like, for example, genetics, chip fabrication, material science, medicine, or chemistry. While highly sophisticated characterization methods would be necessary to study such nanostructures, computational methods and models have made their entrance into the field of nanotechnology. The present work gives an overview of the problems connected with quantum mechanics, many-particle systems, and nanophysical models. Further, the application of molecular dynamics (MD)--a typical computational method suitable for modelling at the nanolevel--is introduced and outlined. The setup and use of specific MD models, advanced computation techniques, and efficient algorithms are discussed, while the focus is laid on the subjects nanodesign and nanoengineering which are demonstrated for the example of metallic nanostructures. Finally, the introduced techniques and methods are applied to stability studies of theoretical nanomachines.
Computer Simulation↗
Ab initio calculation of optical rotation in (P)-(+)-[4]triangulane.
Optical rotation, the angle through which plane-polarized light rotates when passed through an enantiomerically pure medium, plays a vital role in the determination of the absolute configurations of chiral molecules such as natural products. We describe new quantum mechanical methodology designed to assist in this endeavor by providing high-accuracy computational optical rotatory dispersion data for matching to experimental results. Comparison between theory and experiment for the rigid, helical molecule trispiro[2.0.0.2.1.1]nonane [also known as (P)-(+)-[4]triangulane], recently synthesized with enantiomeric purity, shows that the coupled cluster quantum chemical model provides superb agreement for optical rotation across a wide range of wavelengths (589-365 nm), with errors averaging only 1%.
Journal Article↗
Torsional anharmonicity in the conformational analysis of beta-D-galactose.
Schemes to include a treatment of torsional anharmonicity in the conformational analysis of biological molecules are introduced. The approaches combine ab initio electronic energies and harmonic frequencies with anharmonic torsional partition functions calculated using the torsional path integral Monte Carlo method on affordable potential energy surfaces. The schemes are applied to the conformational study of the monosaccharide beta-d-galactose in the gas phase. The global minimum structure is almost exclusively populated at 100 K, but a large number of conformers are present at ambient and higher temperatures. Both quantum mechanical and anharmonic effects in the torsional modes have little effect on the populations at all temperatures considered, and it is, therefore, expected that standard harmonic treatments are satisfactory for the conformational study of monosaccharides.
Galactose↗
Characterization of a single molecular QCA cell by Q-control enhanced amplitude modulation atomic force microscopy.
Major technical challenges for reduction of device sizes for computation and memory are the interconnection and power dissipation problems. Molecular quantum-dot cellular automata (QCA) have been proposed as solutions to this problem. Silicon phthalocyanine (SiPc) is a possible candidate for a molecular QCA element. Therefore, it is important to develop an in situ observation technique to visualize individual SiPc molecules. We report here the first image of a single SiPc dimer in air by using quality factor control (Q-control) enhanced amplitude modulation atomic force microscopy (AFM) and an investigation of the interaction forces between the tip and SiPc dimer. The AFM was operated at 0% relative humidity in an ultrapure nitrogen environment either with or without Q-control. Theoretical simulations using the point-mass description of the AFM, demonstrated that Q-enhancement reduced the force exerted from the tip to the sample surface. Our results, consistent with theory, demonstrated that the image force was reduced and a greater height and a larger size were measured. The advantages of this method can be extended to the AFM observation of other "soft" structures, and these results can be useful for a wider community.
Computers, Molecular↗