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At least 1,045 records · Page 58Linked to original sources
PubMed2005

A computational study of the excited states of bilirubin IX.

We have determined the lowest excited states of bilirubin IX by TD-DFT calculations. The lowest pair of excited states, S(1) and S(2), turn out to be of charge-transfer (CT) nature. Although DFT based methods tend to underestimate the energy of CT states, the small oscillator strengths we have computed indicate that such states may actually exist in this spectral region, but would have escaped spectroscopic detection. The next pair of excited states, S(3) and S(4), account for the most prominent spectral feature of bilirubin. They can be accurately described by the exciton coupling model, as we show by a thorough analysis of wavefunctions and properties. This finding therefore supports the interpretation of bilirubin photoisomerization behaviour, based on the exciton coupling model.

Bilirubin↗
PubMed2005

Theory of the photodissociation of ozone in the Hartley continuum; effect of vibrational excitation and O(1D) atom velocity distribution.

The effect of vibrational excitation on the photodissociation cross section of ozone in the Hartley continuum is examined. The calculations make use of newly computed potential energy and transition dipole moment surfaces. The initial vibrational states of the ozone are computed using grid based techniques and the first few ab initio computed vibrational energy level spacings agree to within 10 cm(-1) with experimental values. The computed total absorption cross sections arising from different initial vibrational states of ozone are discussed in the light of the nature of the transition dipole moment surface. The computed cross section for excitation from the ground vibrational-rotational state is in good agreement with the experimentally measured cross section. Excitation of the asymmetric stretching vibration of ozone has a marked effect on both the form and magnitude of the photodissociation cross section. The velocity distributions of highly reactive O(1D) atoms arising from the photodissociation process in different wavelength ranges is also presented. The results show that the O(1D) atoms travel with a most probable translational velocity of 2.030 km s(-1) corresponding to a translational energy of 0.342 eV or 33.0 kJ mol(-1).

Mathematical Computing↗
PubMed2005

Quantum Brownian motion with large friction.

Quantum Brownian motion in the strong friction limit is studied based on the exact path integral formulation of dissipative systems. In this limit the time-nonlocal reduced dynamics can be cast into an effective equation of motion, the quantum Smoluchowski equation. For strongly condensed phase environments it plays a similar role as master equations in the weak coupling range. Applications for chemical, mesoscopic, and soft matter systems are discussed and reveal the substantial role of quantum fluctuations.

Computer Simulation↗
PubMed2005

Variational grand-canonical electronic structure method for open systems.

An ab initio method is developed for variational grand-canonical molecular electronic structure of open systems based on the Gibbs-Peierls-Boguliobov inequality. We describe the theory and a practical method for performing the calculations within standard quantum chemistry codes using Gaussian basis sets. The computational effort scales similarly to the ground-state Hartree-Fock method. The quality of the approximation is studied on a hydrogen molecule by comparing to the exact Gibbs free energy, computed using full configuration-interaction calculations. We find the approximation quite accurate, with errors similar to those of the Hartree-Fock method for ground-state (zero-temperature) calculations. A further demonstration is given of the temperature effects on the bending potential curve for water. Some future directions and applications of the method are discussed. Several appendices give the mathematical and algorithmic details of the method.

Journal Article↗
PubMed2006

Specific and nonspecific interactions in a molecule with flexible side chain: 2-phenylethanol and its 1:1 complex with argon studied by high-resolution UV spectroscopy.

Using high-resolution resonance-enhanced two-photon ionization spectroscopy in combination with genetic-algorithm-based computer-aided rotational fit analysis and ab initio quantum chemistry calculations we determined the conformational structure and transition moment orientation in 2-phenylethanol and its 1:1 clusters with argon. The results clearly demonstrate that the gauche structure of 2-phenylethanol, which is stabilized by the intramolecular pi-hydrogen bond between the folded side chain and the benzene ring, is the most abundant in the cold molecular beam. In this conformer the transition moment is rotated by 18 degrees from the short axis of the aromatic ring. Two distinct 1:1 complexes of 2-phenylethanol with argon in a cis- and trans-configuration with respect to the side chain have been found. Employing the Kraitchman [Am. J. Phys. 21, 17 (1953)] analysis we have found that the structure of the 2-phenylethanol moiety and the orientation of the transition moment do not change after the complexation with argon within the experimental accuracy. From the measured band intensities we conclude that in addition to the dispersion interaction of the argon atom with the aromatic ring a hydrogen-bond-type interaction with the terminal -OH group of the side chain stabilizes the cis-structure of the 1:1 complex of 2-phenylethanol with argon.

Journal Article↗
PubMed2006

Evidence of the formation and conversion of unstable thionyl isocyanate: Gas-phase spectroscopic studies.

Thionyl diisocyanate which is unstable at ambient temperature is generated from a heterogeneous reaction of gaseous thionyl dichloride with silver cyanate and studied for the first time in the gas phase at 298 K. N-isocyanatoformyl sulfinylimide is also observed with photoelectron spectroscopy in the gas phase for the first time. The conversion of thionyl diisocyanate to N-isocyanatoformyl sulfinylimide via 1,3 shift at different temperatures is studied by using photoelectron spectroscopy and mass spectroscopy with the help of theoretical computations. On the basis of combined observations and quantum chemical calculations, possible 1,3-isocyanato shifts and dissociation processes for thionyl isocyanate and its cation have been discussed in detail.

Electrons↗
PubMed2000

Simple classical mapping of the spin-polarized quantum electron gas: distribution functions and local-field corrections

We use the now well known spin unpolarized exchange-correlation energy E(xc) of the uniform electron gas as the basic "many-body" input to determine the temperature T(q) of a classical Coulomb fluid having the same correlation energy as the quantum system. It is shown that the spin-polarized pair distribution functions (SPDFs) of the classical fluid at T(q), obtained using the hypernetted chain equation, are in excellent agreement with those of the T = 0 quantum fluid obtained by quantum Monte Carlo (QMC) simulations. These methods are computationally simple and easily applied to problems which are currently beyond QMC simulations. Results are presented for the SPDFs and the local-field corrections to the response functions of the electron fluid at T = 0 and finite T.

Journal Article↗
PubMed2004

Appearance of fractional charge in the noise of nonchiral Luttinger liquids.

The current noise of a voltage biased interacting quantum wire adiabatically connected to metallic leads is computed in the presence of an impurity in the wire. We find that in the weak backscattering limit the Fano factor characterizing the ratio between noise and backscattered current crucially depends on the noise frequency omega relative to the ballistic frequency vF/gL, where vF is the Fermi velocity, g is the Luttinger liquid interaction parameter, and L is the length of the wire. In contrast to chiral Luttinger liquids the noise is not only due to the Poissonian backscattering of fractionally charged quasiparticles at the impurity, but it also depends on Andreev-type reflections at the contacts, so that the frequency dependence of the noise needs to be analyzed to extract the fractional charge e*=eg of the bulk excitations.

Journal Article↗
PubMed2006

MI-QSAR models for prediction of corneal permeability of organic compounds.

AIM: To derive a theoretical model for the prediction of corneal permeability of miscellaneous organic compounds in drug design. METHODS: A training set of 28 structurally diverse compounds was used to build up the membrane-interaction quantitative structure-activity relationship (MI-QSAR) models. Intermolecular and intramolecular solute descriptors were computed using molecular mechanics, molecular dynamics simulations and quantum chemistry. The QSAR models were optimized using multidimensional linear regression fitting and a stepwise method. A test set of 8 compounds was evaluated using the models as part of a validation process. RESULTS: Significant MI-QSAR models (R=0.976, S=0.1301, F=70.957) of corneal permeability of organic compounds were constructed. Corneal permeability was found to depend upon the sum of net atomic charges of hydrogen atoms attached to the heteroatoms (N, O), the sum of the absolute values of the net atomic charges of oxygen and nitrogen atoms, the principal moment of inertia (X), the Connolly accessible area and the conformational flexibility of the solute-membrane complex. CONCLUSION: The MI-QSAR models indicated that the corneal permeability of organic molecules was not only influenced by the organic solutes themselves, but also related to the properties of the solute-membrane complex, that is, the interactions of the molecule with the phospholipid-rich regions of cellular membranes.

Animals↗
PubMed2003

Carbon tunneling from a single quantum state.

We observed ring expansion of 1-methylcyclobutylfluorocarbene at 8 kelvin, a reaction that involves carbon tunneling. The measured rate constants were 4.0 x 10(-6) per second in nitrogen and 4 x 10(-5) per second in argon. Calculations indicated that at this temperature the reaction proceeds from a single quantum state of the reactant so that the computed rate constant has achieved a temperature-independent limit. According to calculations, the tunneling contribution to the rate is 152 orders of magnitude greater than the contribution from passage over the barrier. We discuss environmental effects of the solid-state inert-gas matrix on the reaction rate.

Journal Article↗
PubMed1993

Optoelectronic implementation of neural networks.

The performance of electronic neural networks will eventually be limited by the capacity of their interconnections as operating speeds are increased. The use of optical connections to link electronic elements offers a way to overcome this problem. In particular, spatial optic techniques are especially suited to neural systems because of their parallel structure. Three experimental optoelectronic networks are described that employ holographic components and arrays of high-speed optical modulators. These of a network to 64 x 8 connections with optical fan-out. A hybrid networks have been used to demonstrate operation at 50 MHz, novel training algorithms and the expansion technique for integrating optoelectronic systems is also being developed.

Algorithms↗
PubMed2001

Stabilization of the hydrophilic sphere of non-ionic monomers: are all protected in a similar way?

The present study attempts to investigate whether incorporation of a methyl group as second substituent in the tertiary amido group of the two benzamide side chains of iobitridol (Xenetix) increases the stability of the hydrophilic sphere around this molecule as claimed by its manufacturer, and whether this hydrophilic sphere is unique to this particular molecule or to what extent other monomer non-ionic contrast media show this feature. Five non-ionic monomer contrast medium molecules, ioversol, iohexol, iobitridol, ioxilan and iopromide, were studied. Barriers to the rotation of acetanilide and benzamide side chains, and to the rotation of the amide bond in the benzamide chains, were calculated at a semi-empirical quantum mechanical level of theory with the Mopac/Ampac computer program. The five studied contrast medium molecules showed very similar energy barriers to the rotation of complete substituent chains (benzamide and acetanilide) around their bond with the benzene ring. The magnitude of the barriers fell in the range of values mentioned in the literature. In conclusion, introduction of a methyl group as second substituent in the tertiary amido group of the benzamide substituent chains of iobitridol does not increase the studied rotation barriers, i.e. it does not seem to stabilize the hydrophilic sphere to a greater extent compared with similar monomer non-ionic molecules. The sphere is shown to exist in all five analysed molecules. Introduction of a group with a more hydrophobic character has to be considered and eventually questioned, bearing in mind that a more hydrophilic molecule interacts to a lesser degree with body systems.

Contrast Media↗
PubMed1996

[Antimicrobial and physico-chemical aspects of antiseptics based on the iodine-polyvinylpyrrolidone complex].

Antimicrobial efficacy of modern antiseptics-iodophores based on the iodine-polyvinylpyrrolidone complex using standard suspension tests and their modifications and screening methods with bacteriophage phi X 174 was studied. The study was completed with molecular modelling of structural and spatial distribution of these substances with the help of computer programme HyperChem 2.0. Using calculation methods of quantum and molecular mechanics the conditions and results of the antimicrobial efficacy of these antiseptics were described.

Anti-Infective Agents, Local↗
PubMed2006

Criticality, the area law, and the computational power of projected entangled pair states.

The projected entangled pair state (PEPS) representation of quantum states on two-dimensional lattices induces an entanglement based hierarchy in state space. We show that the lowest levels of this hierarchy exhibit a very rich structure including states with critical and topological properties. We prove, in particular, that coherent versions of thermal states of any local 2D classical spin model correspond to such PEPS, which are in turn ground states of local 2D quantum Hamiltonians. This correspondence maps thermal onto quantum fluctuations, and it allows us to analytically construct critical quantum models exhibiting a strict area law scaling of the entanglement entropy in the face of power law decaying correlations. Moreover, it enables us to show that there exist PEPS which can serve as computational resources for the solution of NP-hard problems.

Journal Article↗
PubMed2005

Quantum mechanical free energy barrier for an enzymatic reaction.

We discuss problems related to in silico studies of enzymes and show that accurate and converged free energy changes for complex chemical reactions can be computed if a method based on a thermodynamic cycle is employed. The method combines the sampling speed of molecular mechanics with the accuracy of a high-level quantum mechanics method. We use the method to compute the free energy barrier for a methyl transfer reaction catalyzed by the enzyme catechol O-methyltransferase at the level of density functional theory. The surrounding protein and solvent are found to have a profound effect on the reaction, and we show that energies can be extrapolated easily from one basis set and exchange-correlation functional to another. Using this procedure we calculate a barrier of 69 kJ/mol, in excellent agreement with the experimental value of 75 kJ/mol.

Catechol O-Methyltransferase↗
PubMed2004

Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions.

The determination of reaction paths for enzyme systems remains a great challenge for current computational methods. In this paper we present an efficient method for the determination of minimum energy reaction paths with the ab initio quantum mechanical/molecular mechanical approach. Our method is based on an adaptation of the path optimization procedure by Ayala and Schlegel for small molecules in gas phase, the iterative quantum mechanical/molecular mechanical (QM/MM) optimization method developed earlier in our laboratory and the introduction of a new metric defining the distance between different structures in the configuration space. In this method we represent the reaction path by a discrete set of structures. For each structure we partition the atoms into a core set that usually includes the QM subsystem and an environment set that usually includes the MM subsystem. These two sets are optimized iteratively: the core set is optimized to approximate the reaction path while the environment set is optimized to the corresponding energy minimum. In the optimization of the core set of atoms for the reaction path, we introduce a new metric to define the distances between the points on the reaction path, which excludes the soft degrees of freedom from the environment set and includes extra weights on coordinates describing chemical changes. Because the reaction path is represented by discrete structures and the optimization for each can be performed individually with very limited coupling, our method can be executed in a natural and efficient parallelization, with each processor handling one of the structures. We demonstrate the applicability and efficiency of our method by testing it on two systems previously studied by our group, triosephosphate isomerase and 4-oxalocrotonate tautomerase. In both cases the minimum energy paths for both enzymes agree with the previously reported paths.

Algorithms↗