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PubMed2006

Slice imaging of quantum state-to-state photodissociation dynamics of OCS.

Slice imaging experiments are reported for the quantum state-to-state photodissociation dynamics of OCS. Both one-laser and two-laser experiments are presented detecting CO(J) or S((1)D(2)) photofragments from the dissociation of hexapole state-selected OCS(v(2) = 0,1,2 / J = 1,2) molecules. We present data using our recently developed large frame CCD centroiding detector and have implemented a new high speed MCP high voltage pulser with an effective slice width of only 6 ns. Slice images are presented for quantum state-to-state photolysis, near 230 nm, of vibrationally excited OCS(v(2) = 0,1,2). Two-laser pump-probe experiments detecting CO(J = 63 or 64) show a dramatic change in the beta parameter for the same final state of CO(J) when the photolysis energy is reduced by about 1000 cm(-1). We attribute the observed change from large positive to large negative beta to a large increase of the molecular frame deflection angle at very slow recoil velocity, due to a breakdown of the axial recoil. Two-laser experiments on the S((1)D(2)) fragment reveal single well-separated rings in the slice images correlating with individual CO(J) states. Strong polarization effects of the probe laser are observed, both in the angular distribution of the intensity of single S((1)D(2)) rings and in the resolution of the radial velocity distribution. It is shown how the broadening of the velocity distribution can be reduced by a directed ejection of the electron in the ionization process perpendicular to the slice imaging plane. The dissociation energy of OCS(v(2) = 0, J = 0) --> CO(J = 0) + S((1)D(2)) is determined with high accuracy D(0) = (34 608 +/- 24) cm(-1).

Algorithms↗
PubMed2006

Self-trapping of the N-H vibrational mode in alpha-helical polypeptides.

Recent calculations on the formation of self-trapped amide group vibrational states in alpha-helical polypeptides [J. Chem. Phys. 124, 134907 (2006)] are extended to the amide N-H normal mode vibrations. First, the adiabatic N-H vibrational single- and two-exciton states are examined by treating the longitudinal chain coordinates as parameters. Then, in using the multiconfiguration time-dependent Hartree method coupled exciton-chain vibrational quantum dynamics are accounted for. Based on the respective exciton-chain vibrational wave function propagation the infrared transient absorption related to a sequential pump-probe experiment is calculated. The modulation of local amide vibrational energies by the longitudinal chain coordinates is found to have a pronounced effect on the broadening of absorption lines. Moreover, the ultrafast exciton transfer in the system is studied in order to characterize the dynamics of the self-trapped single-exciton states on a time scale below 10 ps.

Computer Simulation↗
PubMed1998

Derivation of class II force fields. VI. Carbohydrate compounds and anomeric effects.

The methodology for deriving class II force fields has been applied to acetal, hemiacetal, and carbohydrate compounds. A set of eighteen model compounds containing one or more anomeric centers was selected for generating the quantum mechanical energy surface, from which the force field was derived and the functional form assessed. The quality of the fit was tested by comparing the energy surface predicted by the force field with ab initio results. Structural, energetic, and dynamic properties (vibrational frequencies) were analyzed. In addition, alpha and beta anomeric equilibrium structures and energies of 2-methoxytetrahydropyran, 2-deoxyribose, and glucose were computed at the HF/6-31G* and higher ab initio levels. These calculations provide test data from molecules outside the training set used to derive the force field. The quantum calculations were used to assess the ability of the class II force field and two quadratic diagonal (class I) force fields, CVFF, and Homans' extension of the AMBER force field, to account for the anomeric effects on the structural and energetic properties of carbohydrate systems. These class I force fields are unable to account for observed structural and energetic trends, exhibiting deviations as large as 5 kcal/mol in relative energies. The class II force field, on the other hand, is shown to reproduce anomeric structural as well as energetic differences. An energy component analysis of this force field shows that the anomeric differences are dominated by torsional energies, although coupling terms, especially angle/torsion, also make significant contributions (roughly 1 kcal/mol in glucose). In addition, the force field accurately accounts for both anomeric and exo-anomeric energy differences in 2-methoxytetrahydropyran, and anomeric energy differences in 2-deoxyribose and glucose.

Carbohydrates↗
PubMed1996

Optical activity of a nucleotide-sensitive tryptophan in myosin subfragment 1 during ATP hydrolysis.

The xanthene probes 5'-iodoacetamido-fluorescein and -tetramethylrhodamine specifically modify skeletal muscle myosin subfragment 1 (S1) at the reactive thiol residue (SH1) and fully quench the fluorescence emission from tryptophan residue 510 (Trp510) in S1 (T.P. Burghardt and K. Ajtai, Biophys. Chem., 60 (1996) 119; K. Ajtai and T.P. Burghardt, Biochemistry, 34 (1995) 15943). The difference between the fluorescence intensity obtained from S1 and probe-modified S1 comes solely from Trp510 in chymotryptic S1, a protein fragment that contains five tryptophan residues. The rotary strength and quantum efficiency of Trp510 were measured using difference signals from fluorescence detected circular dichroism (FDCD) and fluorescence emission spectroscopy. These structure-sensitive signals indicate that the binding of nucleotide or nucleotide analogs to the active site of S1 causes structural changes in S1 at Trp510 and that a one-to-one correspondence exists between Trp510 conformation and transient states of myosin during contraction. The Trp510 rotary strength and quantum efficiency were interpreted structurally in terms of the indole side-chain conformation using model structures and established computational methods.

Adenosine Triphosphate↗
PubMed1999

Proposal of a new PAF pharmacophoric map by the AM1 method.

PAF is a powerful phospholipid-derived autacoid involved in many pathophysiological processes. Many PAF antagonists have been synthesized and assayed for therapeutic purposes. We have synthesized derivatives (5-7), structurally related to WEB 2086 (1), which were rationally designed based on a planar PAF receptor model previously described by Bures et al. (1994; J. Chem. Inf. Comput. Sci. 24, 218-223). However, pharmacological studies revealed that derivatives (5-7) were inactive as PAF antagonists. AM1 quantum calculations of classical PAF antagonists (1-4), as well as of our derivatives (5-7), demonstrated that electronic features alone are unable to explain the lack of the activity of (5-7). These results induced us to propose a new tridimensional PAF receptor pharmacophoric map by analyzing all stable conformations obtained for derivatives (1-4). The interpoint distances (D1-D5) revealed that the lowest-energy conformers of (5-7) had similar geometries to derivatives (1-4). So, these aspects could not explain the inactivity of the compounds (6-7). The proposed model suggests that the best fit of antagonist compounds may involve the participation of a sulfur atom electron lone pair adequately oriented in relation to the plane of a N-aromatic ring present in the compounds investigated.

Azepines↗
PubMed2007

Crystal and molecular structure of 4,6-bis(nitroimino)-1,3,5-triazinan-2-one: theoretical and X-ray studies.

This paper provides an overview of recent progress on structural data on the title compound. Theoretical work based on quantum mechanical calculations was performed to gain some understanding on the heterocyclic tautomerism potentially exhibited by the compound. The computational studies encompassed a wide range of tautomers/conformers, allowing the determination of the most probable molecular structure. In the gas phase, the nitroimine tautomers are computed to be substantially more stable than the nitramine tautomers. Among three plausible nitroimine forms, special attention was given to 4,6-bis(nitroimino)-1,3,5-triazinan-2-one, whose crystal structure was unequivocally solved by X-ray diffraction. The crystals are orthorhombic, space group Pnma with a = 6.187(2)A, b = 13.252(5)A, c = 8.802(4)A, and Z = 4. The structure was solved by direct methods and refined to a final R = 0.0326. The molecule has an approximate mirror plane relating the two symmetry related halves. The nitroimine groups are positioned in a syn-syn conformation. The least-squares (LS) plane of the heterocyclic ring and the nitroimine ([double bond]N-NO2) substituent LS plane make an angle of 10.05(11) degrees. The crystal structure is held together via hydrogen bonds that assemble the molecules in chains running along the b-axis. Every H-atom is involved in bifurcated hydrogen bonds.

Journal Article↗
PubMed2005

Calculating intensities using effective Hamiltonians in terms of Coriolis-adapted normal modes.

The calculation of rovibrational transition energies and intensities is often hampered by the fact that vibrational states are strongly coupled by Coriolis terms. Because it invalidates the use of perturbation theory for the purpose of decoupling these states, the coupling makes it difficult to analyze spectra and to extract information from them. One either ignores the problem and hopes that the effect of the coupling is minimal or one is forced to diagonalize effective rovibrational matrices (rather than diagonalizing effective rotational matrices). In this paper we apply a procedure, based on a quantum mechanical canonical transformation for deriving decoupled effective rotational Hamiltonians. In previous papers we have used this technique to compute energy levels. In this paper we show that it can also be applied to determine intensities. The ideas are applied to the ethylene molecule.

Journal Article↗
PubMed2006

Conserving many body approach to the infinite-U Anderson model.

Using a Luttinger-Ward scheme for interacting gauge particles, we present a conserving many body treatment of a family of fully screened infinite-U Anderson models that has a smooth crossover into the Fermi-liquid state, with a finite scattering phase shift at zero temperature and a Wilson ratio greater than 1. We illustrate our method, computing the temperature dependence of the thermodynamics, resistivity, and electron dephasing rate and discuss its future application to nonequilibrium quantum dots and quantum critical mixed valent systems.

Journal Article↗
PubMed2005

Temperature dependence of isotopic quantum effects in water.

The technique of high energy x-ray diffraction has been used to measure the temperature variation of hydrogen versus deuterium isotopic quantum effects on the structure of water. The magnitude of the effect is found to be inversely proportional to the temperature, varying by a factor of 2.5 over the range 6 to 45 degrees C. In addition, the H216O versus H218O effect has been measured at 26 degrees C and the structural difference shown to be restricted to the nearest neighbor molecular interactions. The results are compared to recent simulations and previously measured isochoric temperature differentials; additionally, implications for H/D substitution experiments are considered.

Computer Simulation↗
PubMed2004

Mixed-state dynamics in one-dimensional quantum lattice systems: a time-dependent superoperator renormalization algorithm.

We present an algorithm to study mixed-state dynamics in one-dimensional quantum lattice systems. The algorithm can be used, e.g., to construct thermal states or to simulate real time evolution given by a generic master equation. Its two main ingredients are (i) a superoperator renormalization scheme to efficiently describe the state of the system and (ii) the time evolving block decimation technique to efficiently update the state during a time evolution. The computational cost of a simulation increases significantly with the amount of correlations between subsystems, but it otherwise depends only linearly on the system size. We present simulations involving quantum spins and fermions in one spatial dimension.

Journal Article↗
PubMedDate not supplied

Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study.

The suitability of the GMIPp energy functional as a fast, efficient method for estimating the hydrogen-bond donor and acceptor propensities of a wide variety of organic compounds is examined. Comparison of the GMIPp values is made with two experimental hydrogen-bond scales: i) the hydrogen-bond basicity scale for N-heteroaromatics in carbon tetrachloride, and ii) the hydrogen-bond acidities for NH/OH donors and hydrogen-bond basicities of N/O acceptors determined in 1,1,1-trichloroethane. Attention is paid to i) the reliability of semiempirical versus ab initio treatments of the quantum mechanical molecule, ii) the role of solvation, and iii) the effect of including the polarization energy component in the calculation of the GMIPp functional. The statistical analysis of the results reveals that the GMIP functional, which combines electrostatic and steric energy components, predicts with reasonable accuracy and computational efficiency the hydrogen-bond strength for a wide variety of compounds.

Computer Simulation↗
PubMed2001

Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions.

Computer modeling has been developed and widely applied in studying molecules of biological interest. The force field is the cornerstone of computer simulations, and many force fields have been developed and successfully applied in these simulations. Two interesting areas are (a) studying enzyme catalytic mechanisms using a combination of quantum mechanics and molecular mechanics, and (b) studying macromolecular dynamics and interactions using molecular dynamics (MD) and free energy (FE) calculation methods. Enzyme catalysis involves forming and breaking of covalent bonds and requires the use of quantum mechanics. Noncovalent interactions appear ubiquitously in biology, but here we confine ourselves to review only noncovalent interactions between protein and protein, protein and ligand, and protein and nucleic acids.

Catalysis↗
PubMed1994

Structure-function studies of DNA damage using ab initio quantum mechanics and molecular dynamics simulation.

Studies of ring-saturated pyrimidine base lesions are used to illustrate an integrated modeling approach that combines quantum-chemical calculations with molecular dynamics simulation. Electronic structure calculations on the lesions in isolation reveal strong conformational preferences due to interactions between equatorial substituents to the pyrimidine ring. Large distortions of DNA should result when these interactions force the methyl group of thymine to assume an axial orientation, as is the case for thymine glycol but not for dihydrothymine. Molecular dynamics simulations of the dodecamer d(CGCGAATTCGCG)2 with and without a ring-saturated thymine lesion at position T7 support this conclusion. Implications of these studies for recognition of thymine lesions by endonuclease III are also discussed.

Base Sequence↗
PubMed2004

Promoting vibrations in human purine nucleoside phosphorylase. A molecular dynamics and hybrid quantum mechanical/molecular mechanical study.

Crystallographic studies of human purine nucleoside phosphorylase (hPNP) with several transition-state (TS) analogues in the immucillin family showed an unusual geometric arrangement of the atoms O-5', O-4', and O(P), the nucleophilic phosphate oxygen, lying in a close three-oxygen stack. These observations were corroborated by extensive experimental kinetic isotope effect analysis. We propose that protein-facilitated dynamic modes in hPNP cause this stack, centered on the ribosyl O-4' oxygen, to squeeze together and push electrons toward the purine ring, stabilizing the oxacarbenium character of the TS. As the N-ribosidic bond is cleaved during the reaction, the pK(a) values of N-7 and O-6 increase by the electron density expelled by the oxygen-stack compression toward the purine ring. Increased electron density in the purine ring improves electrostatic interactions with nearby residues and facilitates the abstraction of a proton from a solvent proton or an unidentified general acid, making the purine a better leaving group, and accelerating catalysis. Classical and mixed quantum/classical molecular dynamics (MD) simulations of the Michaelis complex of hPNP with the substrates guanosine and phosphate were performed to assess the existence of protein-promoting vibrations (PPVs). Analogous simulations were performed for the substrates in aqueous solution. In the catalytic site, the O-5', O-4', and O(P) oxygens vibrate at frequencies of ca. 125 and 465 cm(-1), as opposed to 285 cm(-1) in the absence of hPNP. The hybrid quantum mechanical/molecular mechanical method was used to assess whether this enzymatic vibration pushing the oxygens together is coupled to the reaction coordinate, and thus has a direct positive impact on catalysis. The potential energy surface for the phosphorolysis reaction for several snapshots taken from the classical MD simulation showed substantial differences in oxygen compression. Our calculations showed the existence of PPVs coupled to the reaction coordinate, which effect electronic alterations in the active site by pushing the three oxygen centers together in proximity, and accelerate substrate turnover in the phosphorolysis reaction catalyzed by hPNP.

Animals↗
PubMed2005

Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations.

Special care is needed in carrying out combined quantum mechanical and molecular mechanical (QM/MM) calculations if the QM/MM boundary passes through a covalent bond. The present paper discusses the importance of correctly handling the MM partial point charges at the QM/MM boundary, and in particular, it contributes in two aspects: (1) Two schemes, namely, the redistributed charge (RC) scheme and the redistributed charge and dipole (RCD) scheme, are introduced to handle link atoms in QM/MM calculations. In both schemes, the point charge at the MM boundary atom that is replaced by the link atom is redistributed to the midpoint of the bonds that connect the MM boundary atom and its neighboring MM atoms. These redistributed charges serve as classical mimics for the auxiliary orbitals associated with the MM host atom in the generalized hybrid orbital (GHO) method. In the RCD scheme, the dipoles of these bonds are preserved by further adjustment of the values of the redistributed charges. The treatments are justified as classical analogues of the QM description given by the GHO method. (2) The new methods are compared quantitatively to similar methods that were suggested by previous work, namely, a shifted-charge scheme and three eliminated-charge schemes. The comparisons were carried out for a series of molecules in terms of proton affinities and geometries. Point charges derived from various charge models were tested. The results demonstrate that it is critical to preserve charge and bond dipole and that it is important to use accurate MM point charges in QM/MM boundary treatments. The RCD scheme was further applied to study the H atom transfer reaction CH3 + CH3CH2CH2OH --> CH4 + CH2CH2CH2OH. Various QM levels of theory were tested to demonstrate the generality of the methodology. It is encouraging to find that the QM/MM calculations obtained a reaction energy, barrier height, saddle-point geometry, and imaginary frequency at the saddle point in quite good agreement with full QM calculations at the same level. Furthermore, analysis based on energy decomposition revealed the quantitatively similar interaction energies between the QM and the MM subsystems for the reactant, for the saddle point, and for the product. These interaction energies almost cancel each other energetically, resulting in negligibly small net effects on the reaction energy and barrier height. However, the charge distribution of the QM atoms is greatly affected by the polarization effect of the MM point charges. The QM/MM charge distribution agrees much better with full QM results than does the unpolarized charge distribution of the capped primary subsystem.

Chemistry, Physical↗
PubMed2005

Ab initio quantum mechanical study of the binding energies of human estrogen receptor alpha with its ligands: an application of fragment molecular orbital method.

We have theoretically examined the relative binding affinities (RBA) of typical ligands, 17beta-estradiol (EST), 17alpha-estradiol (ESTA), genistein (GEN), raloxifene (RAL), 4-hydroxytamoxifen (OHT), tamoxifen (TAM), clomifene (CLO), 4-hydroxyclomifene (OHC), diethylstilbestrol (DES), bisphenol A (BISA), and bisphenol F (BISF), to the alpha-subtype of the human estrogen receptor ligand-binding domain (hERalpha LBD), by calculating their binding energies. The ab initio fragment molecular orbital (FMO) method, which we have recently proposed for the calculations of macromolecules such as proteins, was applied at the HF/STO-3G level. The receptor protein was primarily modeled by 50 amino acid residues surrounding the ligand. The number of atoms in these model complexes is about 850, including hydrogen atoms. For the complexes with EST, RAL, OHT, and DES, the binding energies were calculated again with the entire ERalphaLBD consisting of 241 residues or about 4000 atoms. No significant difference was found in the calculated binding energies between the model and the real protein complexes. This indicates that the binding between the protein and its ligands is well characterized by the model protein with the 50 residues. The calculated binding energies relative to EST were very well correlated with the experimental RBA (the correlation coefficient r=0.837) for the ligands studied in this work. We also found that the charge transfer between ER and ligands is significant on ER-ligand binding. To our knowledge, this is the first achievement of ab initio quantum mechanical calculations of large molecules such as the entire ERalphaLBD protein.

Binding Sites↗
PubMed2005

Quantum chemical study of three polymorphs of the mononuclear spin-transition complex [Fe(DPPA)(NCS)2].

The calculations of the high spin (HS) and low spin (LS) states of the [Fe(II)(DPPA)(NCS)(2)] complex have been performed at three experimentally observed geometries corresponding to three synthesized polymorphs with different spin-transition behavior. The structure optimization leads to a single molecular structure, suggesting that the existence of three geometries is not an intrinsic phenomenon but is induced by the crystal lattice. The structural difference between three forms can be reproduced by introducing the Madelung field of the crystal lattice. However, the calculations show that the differences in magnetic behavior of the three polymorphs cannot be attributed only to variations of the energy gap between two spin states.

Computer Simulation↗
PubMed2002

Electromagnetic fields on a quantum scale. I.

This is the first in a series of two articles, the second of which provides an exact electro-magnetic field description of photon emission, absorption, and radiation pattern. Photon energy exchanges are analyzed and shown to be the triggered, regenerative response of a non-local eigenstate electron. This first article presents a model-based, hidden variable analysis of quantum theory that provides the statistical nature of wave functions. The analysis uses the equations of classical electro-magnetism and conservation of energy while modeling an eigenstate electron as a nonlocal entity. Essential to the analysis are physical properties that were discovered and analyzed only after the historical interpretation of quantum mechanics was established: electron non-locality and the standing electro-magnetic energy that accompanies and encompasses an active, electrically small volume. The standing energy produces a driving radiation reaction force that, under certain circumstances, is many orders of magnitude larger than currently accepted values. These properties provide a sufficient basis for the Schrödinger equation as a descriptor of non-relativistic eigenstate electrons in or near equilibrium. The uncertainty principle follows, as does the exclusion principle. The analysis leads to atomic stability and causality in the sense that the status of physical phenomena at any instant specifies the status an instant later.

Computer Simulation↗

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