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At least 1,027 records · Page 57Linked to original sources
PubMed2006

Solvent effect on the singlet excited-state lifetimes of nucleic acid bases: A computational study of 5-fluorouracil and uracil in acetonitrile and water.

The first comprehensive quantum mechanical study of solvent effects on the behavior of the two lowest energy excited states of uracil derivatives is presented. The absorption and emission spectra of uracil and 5-fluorouracil in acetonitrile and aqueous solution have been computed at the time-dependent density-functional theory level, using the polarizable continuum model (PCM) to take into account bulk solvent effects. The computed spectra and the solvent shifts provided by our method are close to their experimental counterpart. The S0/S1 conical intersection, located in the presence of hydrogen-bonded solvent molecules by CASSCF (8/8) calculations, indicates that the mechanism of ground-state recovery, involving out-of-plane motion of the 5 substituent, does not depend on the nature of the solvent. Extensive explorations of the excited-state surfaces in the Franck-Condon (FC) region show that solvent can modulate the accessibility of an additional decay channel, involving a dark n/pi* excited state. This finding provides the first unifying explanation for the experimental trend of 5-fluorouracil excited-state lifetime in different solvents. The microscopic mechanisms underlying solvent effects on the excited-state behavior of nucleobases are discussed.

Absorption↗
PubMed2002

Ultra low dose X-ray spinal examinations.

The study and treatment of spinal deformities may lead to excessive doses of radiation for patients (especially children) examined by conventional X-ray radiology apparatus. In order to avoid this very crucial problem, a new X-ray radiology system has been devised. The new apparatus uses a high efficiency linear solid-state detector and highly sensitive electronics, operating in single X-ray counting mode (quantum mode). The scan parameters and image filtering are computer controlled. Data is acquired in real time by a high speed VME system. In this paper, the first images recorded using this new apparatus are shown. The main conclusion of the preliminary comparative dosimetric analysis is that it is possible to divide the patient's dose by a factor of at least ten to one hundred with the quantum X-ray radiology apparatus.

Humans↗
PubMed1998

Signal, noise power spectrum, and detective quantum efficiency of indirect-detection flat-panel imagers for diagnostic radiology.

The performance of an indirect-detection, active matrix flat-panel imager (FPI) at diagnostic energies is reported in terms of measured and theoretical signal size, noise power spectrum (NPS), and detective quantum efficiency (DQE). Based upon a 1536 x 1920 pixel, 127 microns pitch array of a-Si:H thin-film transistors and photodiodes, the FPI was developed as a prototype for examination of the potential of flat-panel technology in diagnostic x-ray imaging. The signal size per unit exposure (x-ray sensitivity) was measured for the FPI incorporating five commercially available Gd2O2S:Tb converting screens at energies 70-120 kVp. One-dimensional and two-dimensional NPS and DQE were measured for the FPI incorporating three such converters and as a function of the incident exposure. The measurements support the hypothesis that FPIs have significant potential for application in diagnostic radiology. A cascaded systems model that has shown good agreement with measured individual pixel signal and noise properties is employed to describe the performance of various FPI designs and configurations under a variety of diagnostic imaging conditions. Theoretical x-ray sensitivity, NPS, and DQE are compared to empirical results, and good agreement is observed in each case. The model is used to describe the potential performance of FPIs incorporating a recently developed, enhanced array that is commercially available and has been proposed for testing and application in diagnostic radiography and fluoroscopy. Under conditions corresponding to chest radiography, the analysis suggests that such systems can potentially meet or even exceed the DQE performance of existing technology, such as screen-film and storage phosphor systems; however, under conditions corresponding to general fluoroscopy, the typical exposure per frame is such that the DQE is limited by the total system gain and additive electronic noise. The cascaded systems analysis provides a valuable means of identifying the limiting stages of the imaging system, a tool for system optimization, and a guide for developing strategies of FPI design for various imaging applications.

Equipment Design↗
PubMed2007

Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations.

A potential scaling version of simulated tempering is presented to efficiently sample configuration space in a localized region. The present "simulated scaling" method is developed with a Wang-Landau type of updating scheme in order to quickly flatten the distributions in the scaling parameter lambdam space. This proposal is meaningful for a broad range of biophysical problems, in which localized sampling is required. Besides its superior capability and robustness in localized conformational sampling, this simulated scaling method can also naturally lead to efficient "alchemical" free energy predictions when dual-topology alchemical hybrid potential is applied; thereby simultaneously, both of the chemically and conformationally distinct portions of two end point chemical states can be efficiently sampled. As demonstrated in this work, the present method is also feasible for the quantum mechanical and quantum mechanical/molecular mechanical simulations.

Algorithms↗
PubMed2004

A sequential molecular mechanics/quantum mechanics study of the electronic spectra of amides.

We report gas-phase electronic spectra of formamide, N-methyformamide, acetamide, and N-methylacetamide at 300 K calculated using a combination of classical molecular dynamics and time-dependent density functional theory (TDDFT). In comparison to excitation energies computed using the global minima structures, the valence npi* and pi(nb)pi* states show a significant red-shift of 0.1-0.35 eV, while smaller shifts are found for the n3s and pi(nb)3s Rydberg states. In this work, we have identified the physical origin of these shifts arising from variations of the molecular structure. We present simple relationships between key geometrical parameters and spectral shifts. Consequently, electronic spectra can be generated directly from ground-state structures, without additional quantum chemical calculations. The electronic spectrum of formamide in aqueous solution is computed using TDDFT using an explicit solvent model. This provides a quantitative determination of the condensed-phase spectrum. In general, this study shows that temperature effects can change the predicted excitation energies significantly and demonstrates how electronic spectra at elevated temperatures can be computed in a computationally efficient way.

Amides↗
PubMed2006

Nonadiabatic trajectory studies of NaI(H2O)n photodissociation dynamics.

We have investigated the photodissociation dynamics of NaI(H(2)O)(n) [n = 1-4] clusters using the molecular dynamics with quantum transitions method and a quantum mechanics/molecular mechanics description of NaI(H(2)O)(n), which involves a semiempirical valence-bond approach to describe the NaI electronic structure and classical solvent-solvent and solute-solvent interaction potentials. Our simulation results show that the NaI(H(2)O)(n) excited-state population decay upon reaching the NaI curve-crossing region increases with cluster size due to the stabilization of the ionic branch of the NaI excited state by the surrounding water molecules, and the resulting increase in nonadiabatic transition probability. After reaching the curve-crossing region for the first time, however, the excited-state population decay resembles that of bare NaI because of rapid evaporation of 99% and 95% of the water molecules for NaI(H(2)O) and NaI(H(2)O)(n) [n = 2-4], respectively. This extensive evaporation is due to the reversed NaI polarity in the Franck-Condon region of the NaI first excited state, which causes strong repulsive NaI-H(2)O forces and induces rapid nonstatistical water evaporation, where product water molecules are formed more rotationally than translationally hot. A few water molecules (5% or less) remain transiently or permanently bound to NaI, forming long-lived clusters, when NaI remains predominantly ionic, i.e., remains in the excited state, after reaching the curve-crossing region. To connect simulation results with experiment, we have simulated femtosecond probe signals resulting from two-photon and one-photon excitation to the X and I NaI(+) probe states. In agreement with experimental findings, the probe signals resulting from the two-photon probe scheme, where excitation occurs from the covalent branch of the excited state, decay exponentially over the NaI first excited-state vibrational period, with very little evidence of long-time dynamics. The one-photon probe scheme (not used for experimental cluster studies) is shown to be less sensitive to solvation, in that excitation energies will remain similar over a range of cluster sizes, as the ionic branch of the excited state and the NaI(+) probe states are stabilized to the same extent by the presence of water molecules. The resulting probe signals are also more revealing of the NaI(H(2)O)(n) photodissociation dynamics than the two-photon probe signals, as they may allow monitoring of solvation effects on the NaI nonadiabatic dynamics and of successive evaporation of water molecules. Time-resolved photoelectron spectra provide limited additional information regarding the NaI(H(2)O)(n) photodissociation dynamics. A key consequence of the rapid water evaporation demonstrated here is that experimentally observed signals may arise from the photodissociation of much larger NaI(H(2)O)(n) parent clusters.

Computer Simulation↗
PubMed2004

Shot noise of a quantum shuttle.

We formulate a theory for shot noise in quantum nanoelectromechanical systems. As a specific example, the theory is applied to a quantum shuttle, and the zero-frequency noise, measured by the Fano factor F, is computed. F reaches very low values (F approximately 10(-2)) in the shuttling regime even in the quantum limit, confirming that shuttling is universally a low noise phenomenon. In approaching the semiclassical limit, the Fano factor shows a giant enhancement (F approximately 10(2)) at the shuttling threshold, consistent with predictions based on phase-space representations of the density matrix.

Journal Article↗
PubMed2002

Optical rotation: recent advances in determining the absolute configuration.

The field of optical rotations is currently undergoing a renaissance, which is a direct result of the advances in quantum mechanics and the availability of faster desktop computers. In the last few years, the field of optical rotations has taken an important role for determining the three-dimensional molecular structure (absolute configuration and conformations) with confidence. The purpose of this review is to present the latest advances in this area so that practicing chemists can utilize them in their respective areas of research and development.

Journal Article↗
PubMed2003

A multicentered approach to integrated QM/QM calculations. Applications to multiply hydrogen bonded systems.

A multicentered integrated QM/QM technique has been developed. By separating high-level calculations in distinct regions of molecules, the multicentered approach supplants a single large high-level calculation with several smaller calculations. Due to the steep polynomial scaling of traditional ab initio quantum chemical methods, this separation significantly enhances the computational efficiency of QM/QM methods. The straightforward implementation of this multicentered approach is illustrated with several large poly-alcohols that form hydrogen bonds with water. The largest alcohol-water complex contains 81 atoms. For properly selected model systems, this multicentered approach introduces essentially no error in the dissociation energies of these complexes relative to conventional QM/QM schemes. This multicentered technique should be easily extended to other, more general integrated methods (QM/MM, ONIOM, etc).

Journal Article↗
PubMed2004

Fast fragments: the development of a parallel effective fragment potential method.

The Effective Fragment Potential (EFP) method for solvation decreases the cost of a fully quantum mechanical calculation by dividing a chemical system into an ab initio region that contains the solute plus some number of solvent molecules, if desired, and an "effective fragment" region that contains the remaining solvent molecules. Interactions introduced with this fragment region (for example, Coulomb and polarization interactions) are added as one-electron terms to the total system Hamiltonian. As larger systems and dynamics are just starting to be studied with the EFP method, more needs to be done to decrease the calculation time of the method. This article considers parallelization of both the EFP fragment-fragment and mixed quantum mechanics (QM)-EFP interaction energy and gradient computation within the GAMESS suite of programs. The iteratively self-consistent polarization term is treated with a new algorithm that makes use of nonblocking communication to obtain better scalability. Results show that reasonable speedup is achieved with a variety of sizes of water clusters and number of processors.

Journal Article↗
PubMed2005

A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides.

Recently, the importance of proline ring pucker conformations in collagen has been suggested in the context of hydroxylation of prolines. The previous molecular mechanics parameters for hydroxyproline, however, do not reproduce the correct pucker preference. We have developed a new set of parameters that reproduces the correct pucker preference. Our molecular dynamics simulations of proline and hydroxyproline monomers as well as collagen-like peptides, using the new parameters, support the theory that the role of hydroxylation in collagen is to stabilize the triple helix by adjusting to the right pucker conformation (and thus the right phi angle) in the Y position.

Collagen↗
PubMed2006

The VMFCI method: a flexible tool for solving the molecular vibration problem.

The present article introduces a general variational scheme to find approximate solutions of the spectral problem for the molecular vibration Hamiltonian. It is called the "vibrational mean field configuration interaction" (VMFCI) method, and consists in performing vibrational configuration interactions (VCI) for selected modes in the mean field of the others. The same partition of modes can be iterated until self-consistency, generalizing the vibrational self-consistent field (VSCF) method. As in contracted-mode methods, a hierarchy of partitions can be built to ultimately contract all the modes together. So, the VMFCI method extends the traditional variational approaches and can be included in existing vibrational codes based on the latter approaches. The flexibility and efficiency of this new method are demonstrated on several molecules of atmospheric interest.

Computer Simulation↗
PubMed2004

A DFT-based QSARs study of protoporphyrinogen oxidase inhibitors: phenyl triazolinones.

The equilibrium geometries, electronic structures, and electrostatic potentials of a series of substituted phenyl triazolinones, a kind of important protoporphyrinogen oxidase (Protox) inhibitors, had been investigated using density functional theory (DFT) method at the B3LYP/6-31G(d,p) basis set. The quantum chemical descriptors, such as energy difference (DeltaE) between the lowest unoccupied molecular orbital and the highest occupied molecular orbital, electrophilic and nucleophilic frontier electron density (f(i)(E) and f(i)(N)), and net atomic charge (Q(i)), were computed at the same DFT level. Based on these useful quantum chemical descriptors, the quantitative structure-activity relationships was carried out and the results showed that descriptors, Q(C11), f(N5)(E), f(C10)(N), f(O6)(E), f(C11)(N), and DeltaE, were most likely to be responsible for the in vitro biological activity and the greenhouse pre-emergence activity of phenyl triazolinones. The descriptors accounted for 77-86% of the variation in the in vitro biological activity among the herbicidal phenyl triazolinone analogs 1-26 (except compounds 19 and 20). The results of the regression analysis showed that the activity was parabolically related not only with the descriptor f(O6)(E), but also with the descriptor f(C11)(N) . The optimum values of the terms f(O6)(E) and f(C11)(N) were about 11.15 and 0, respectively. Studies also showed that compound 19 exhibiting the highest in vitro activity mimicked the three-ring portion of protoporphyrinogen IX (Protogen). The present work had proved that the DFT-based quantum chemical descriptors could lead to the better correlation relationship than that the PM3-based electronic descriptors, therefore, DFT-based QSARs could be expected to help facilitate the design of additional substituted phenyl triazolinone derivatives of Protox inhibitors with good biological activity.

Enzyme Inhibitors↗
PubMed2004

3,5-Pyridyne--a heterocyclic meta-benzyne derivative.

3,5-Pyridyne (3) has been generated by flash vacuum pyrolysis of 3,5-diiodopyridine (20) and 3,5-dinitropyridine (21) and characterized by IR spectroscopy in cryogenic argon matrices. The aryne can clearly be distinguished from other side products by its photolability at 254 nm, inducing a rapid ring-opening presumably to (Z)-1-aza-hex-3-ene-1,5-diyne. As byproducts of the pyrolysis, HCN and butadiyne were identified, together with traces of acetylene, cyanoacetylene, (E)-1-aza-hex-3-ene-1,5-diyne, and the 3-iodo-5-pyridyl radical (from 20). Several pathways for rearrangements and fragmentations of 3 and of the parent meta-benzyne (1) have been explored computationally by density functional theory and ab initio quantum chemical methods. The lowest energy decomposition pathway of biradicals 1 and 3 is a ring-opening process accompanied by hydrogen migration, leading to (Z)-hex-3-ene-1,5-diyne [(Z)-10] and (Z)-3-aza-hex-3-ene-1,5-diyne [(Z)-24], respectively. Both reactions require activation energies of 45-50 kcal mol(-1). Mechanisms leading from (Z)-24 or directly from 3 to the experimentally observed byproducts are discussed. Upon replacement of the C(5)H moiety by N in meta-benzyne, high-level calculations predict a modest shortening of the interradical distance by 5-7 pm and a reduction of the singlet-triplet energy splitting by 3 kcal mol(-1), in good agreement with isodesmic equations, according to which the singlet ground state of 3 is destabilized relative to 1 by 3-4 kcal mol(-1). In contrast to 3,5-borabenzyne (2), which is found to be doubly aromatic, nucleus-independent chemical shifts of 3 are almost identical to that of pyridine, indicating the absence of paramagnetic ring current effects that may be associated with "in-plane antiaromaticity". As compared with 1, the overall perturbation caused by the nitrogen atom in 3 is weak, and four electron, three center interaction is of minor importance in this molecule.

Journal Article↗
PubMed1979

Computer-assisted structure-activity studies of chemical carcinogens. A heterogeneous data set.

A structure-activity relations study has been performed on a heterogeneous set of organic compounds to develop predictive ability for carcinogenic potential. The compounds employed came from more than 12 structural classes and numbered 130 carcinogens and 79 noncarcinogens. A set of 28 calculated molecular structure descriptors was identified that supported a linear discriminant function able to completely separate 192 compounds into the carcinogenic and noncarcinogenic classes. A predictive ability of 90% for carcinogens and 78% for noncarcinogens was obtained in randomized testing. The results demonstrate that pattern-recognition methods can be used to analyze a diverse set of compounds each represented by calculated molecular structure descriptors for a common biological activity.

Carcinogens↗
PubMed2003

On the aromatic character of the heterocyclic bases of DNA and RNA.

Studies based on ab initio optimized geometries (at B3LYP/6-311+G** and MP2/6-311+G** levels) and on experimental structures retrieved from the Cambridge Structural Database (CSD) reveal that the nucleobases constituting DNA and RNA differ significantly in their aromatic character, as shown by the geometry-based index of aromaticity HOMA that ranges from 0.466 for thymine to 0.917 for adenine, based on B3LYP/6-311+G** calculations, and 0.495-0.926, respectively, if based on the MP2/6-311+G** level. Aromaticity of the bases decreases markedly with an increase of the number of double-bond C=X (X = N, O) substituents at the rings. H-bonds involving C=O groups in Watson-Crick pairs cause an increase of the aromatic character of the rings.

Adenine↗
PubMed2006

Computational studies on stable triplet states of heteroacetylenes and the effects of halogen substituents.

This paper describes theoretical studies of halogen-substituted heteroacetylenes (XCMY, M = Si and Ge; X, Y = H, Cl and F) performed at the QCISD(T)/6-311G//QCISD/6-31G level of theory. The electronegative halogen substituents destabilize the singlet state such that the triplet state tends to become favorable. The triplet state has the bifunctional electronic structure of a triplet carbene joined to a heavy singlet carbene. We found that the substituents effectively reduce the energy of the donor-acceptor interactions (E(D-A)) between the two in-plane lone pairs of electrons of the singlet state; therefore, the remaining pi bond is less favorable energetically than the triplet state with a sigma bond. A related phenomenon occurs for the homonuclear heavy acetylenes in singlets in which the lead compound RPbPbR switches to a Pb-Pb sigma bond from the pi bonds observed for the lighter acetylenes.

Alkynes↗