Nuclear Geometry Research Articles

Charge migration in different conformers of glycine: The role of nuclear geometry

The migration of hole charge created via ionization of the main conformers of the gaseous amino acid glycine is studied. The migration is ultrafast and is mediated solely by many-electron effects, i.e. electronic correlation and relaxation. The influence of the nuclear geometry is investigated by studying the three most abundant conformers of glycine. It is shown that the electron dynamics following ionization can be dramatically different for the different conformers. To facilitate the discussion of the charge migration, the ionization spectra of the conformers are computed as well.

Unique helical conformation of the fourth cytoplasmic loop of the CB 1 cannabinoid receptor in a negatively charged environment

The proximal portion of the C-terminus of the CB 1 cannabinoid receptor is a primary determinant for G-protein activation. A 17 residue proximal C-terminal peptide (rodent CB1 401–417), the intracellular loop 4 (IL4) peptide, mimicked the receptor’s G-protein activation domain. Because of the importance of the cationic amino acids to G-protein activation, the three-dimensional structure of the IL4 peptide in a negatively charged sodium dodecyl sulfate (SDS) micellar environment has been studied by two-dimensional proton nuclear magnetic resonance (2D 1H NMR) spectroscopy and distance geometry calculations. Unambiguous proton NMR assignments were carried out with the aid of correlation spectroscopy (DQF-COSY and TOCSY) and nuclear Overhauser effect spectroscopy (NOESY and ROESY) experiments. The distance constraints were used in torsion angle dynamics algorithm for NMR applications (DYANA) to generate a family of structures which were refined using restrained energy minimization and dynamics. In water, the IL4 peptide prefers an extended conformation, whereas in SDS micelles, 3 10-helical conformation is induced. The predominance of 3 10-helical domain structure in SDS represents a unique difference compared with structure in alternative environments, which can significantly impact global electrostatic surface potential on the cytoplasmic surface of the CB 1 receptor and might influence the signal to the G-proteins.

Electron–phonon interactions and intrinsic nonadiabatic state of superconductors

Study of band structure of YBa 2Cu 3O 7 has shown that electron coupling to A g, B 2g and B 3g modes results in fluctuation of saddle point of one of the CuO plane d-pσ band in Y point of 1st BZ across Fermi level. It represents breakdown of adiabatic Born–Oppenheimer approximation and transition of the system into intrinsic nonadiabatic state, ω > E F. Results show that system is stabilized in this state at distorted nuclear geometry. Stabilization effect is mainly due to strong dependence of the electronic motion on instantaneous nuclear momenta. On the lattice scale, the intrinsic nonadiabatic state is geometrically degenerate at broken translation symmetry – system has fluxional nuclear configuration of O2, O3 atoms in CuO planes. It enables formation of mobile bipolarons that can move in the lattice without dissipation. Described effects are absent in non-superconducting YBa 2Cu 3O 6.

Resolving the plasma profile via differential single inclusive suppression

The ability of experimental signatures to resolve the spatiotemporal profile of an expanding quark-gluon plasma is studied. In particular, the single inclusive suppression of high-momentum hadrons versus the centrality of a heavy-ion collision and with respect to the reaction plane in noncentral collisions is critically examined. Calculations are performed in the higher twist formalism for the modification of the fragmentation functions. Radically different nuclear geometries are used. The influence of different initial gluon distributions as well as different temporal evolution scenarios on the single inclusive suppression of high-momentum pions are outlined. It is demonstrated that the modification versus the reaction plane is quite sensitive to the initial spatial density. Such sensitivity remains even in the presence of a strong elliptic flow.

OviAsymmetry and an Accelerated Outflow in an Obscured Seyfert:FUSEandHSTSTIS Spectroscopy of Mrk 533

We present far-ultraviolet spectra of the Seyfert 2 galaxy Mrk 533 obtained with FUSE. These spectra show narrow asymmetrical O VI λλ1032,1038 emission lines with stronger wings shortward of the peak wavelength, but the degree of asymmetry of these wings in velocity is much lower than that of the wings of the lines of lower ionization. In the combined O VI profile there are marginal indications of local absorptions in the outflow. The C III λ977 line is seen weakly with a similar profile, but with very low signal-to-noise ratio (S/N). These FUV spectra are among the first for a Seyfert of type 2, i.e., a purportedly obscured Seyfert. The HST STIS spectral image of Mrk 533 allows delineation of the various components of the outflow, and we infer that the outflow is accelerated. We discuss the results in terms of nuclear geometry and kinematics.

Angular dependence of dissociative electron attachment to polyatomic molecules: Application to theB12metastable state of theH2OandH2Sanions

The angular dependence of dissociative electron attachment (DEA) to polyatomic targets is formulated in the local complex potential model, under the assumption that the axial recoil approximation describes the dissociation dynamics. An additional approximation, which is found to be valid in the case of ${\mathrm{H}}_{2}\mathrm{O}$ but not in the case of ${\mathrm{H}}_{2}\mathrm{S}$, makes it possible to describe the angular dependence of DEA solely from an analysis of the fixed-nuclei entrance amplitude, without carrying out nuclear dynamics calculations. For ${\mathrm{H}}_{2}\mathrm{S}$, the final-vibrational-state-specific angular dependence of DEA is obtained by incorporating the variation of the angular dependence of the entrance amplitude with nuclear geometry into the nuclear dynamics. Scattering calculations using the complex Kohn method and, for ${\mathrm{H}}_{2}\mathrm{S}$, full quantum calculations of the nuclear dynamics using the multiconfiguration time-dependent Hartree method, are performed.

Intriguing accuracies of the exponential wave function expansions exploiting finite two-body correlation operators in calculations for many-electron systems

Following the ideas laid down by Nooijen and Nakatsuji, several authors have considered an intriguing possibility of representing the exact many-electron wave functions by the exponential cluster expansions involving two-body correlation operators. In particular, inspired by the symmetric form of the Horn–Weinstein exact energy formula, and exploiting the variational principle and numerical analysis, we have demonstrated that one can obtain nearly exact ground-state wave functions for a few many-electron systems using the exponential cluster expansion involving a finite two-body operator acting on the Hartree–Fock determinant [P. Piecuch et al., Phys. Rev. Lett. 90 (2003) 113001]. After summarizing these earlier findings and making some additional comments on the nature of the exponential cluster expansions involving two-body correlation operators, we examine the following issues: (i) the improvements in the accuracy and convergence toward the full configuration interaction (CI) limit offered by cluster operators containing two-body as well as one-body components, (ii) the improvements in the accuracy resulting from the use of multi-determinantal reference states, and (iii) the potential accuracy of the exponential wave function expansions involving finite one- and two-body cluster operators in excited-state calculations. All calculations are performed for an eight electron model system, which is simple enough to allow for the exact, full CI, and other electronic structure calculations, which has fewer independent parameters in the Hamiltonian than the dimension of the corresponding full CI problem, and which enables one to examine ground and excited states with a varying degree of configurational quasi-degeneracy by simple changes in the corresponding nuclear geometry.

Direct calculation of coupled diabatic potential-energy surfaces for ammonia and mapping of a four-dimensional conical intersection seam

We used multiconfiguration quasidegenerate perturbation theory and the fourfold-way direct diabatization scheme to calculate ab initio potential-energy surfaces at 3600 nuclear geometries of NH3. The calculations yield the adiabatic and diabatic potential-energy surfaces for the ground and first electronically excited singlet states and also the diabatic coupling surfaces. The diabatic surfaces and coupling were fitted analytically to functional forms to obtain a permutationally invariant 2 x 2 diabatic potential-energy matrix. An analytic representation of the adiabatic potential-energy surfaces is then obtained by diagonalizing the diabatic potential-energy matrix. The analytic representation of the surfaces gives an analytic representation of the four-dimensional conical intersection seam which is discussed in detail.

Rules on the changes of approximate symmetry measures along reaction paths†

A theorem is proven, describing the differences in the gradual emergence of different symmetry elements of non-symmetric molecular structures as the nuclear geometries change along reaction paths. The gradual establishment of individual symmetry elements is described in terms of the rates of convergence of symmetry deficiency measures along steepest descent paths leading to a critical point. This critical point may be a minimum or a saddle point of any index of the potential energy hypersurface, as long as the steepest descent path leads to it. If within a quadratic neighbourhood of the critical point the local internal coordinates are given in terms of the eigenvectors of the Hessian matrix, then the theorem asserts that, for any distorted nuclear arrangement displaced along a steepest descent path within the quadratic neighbourhood of a critical point, the symmetry element that is present along the eigenvector of the lowest positive eigenvalue of the Hessian is restored the fastest, at an exponential rate relative to the restoration rate of other distorted symmetry elements. Although it is only an apparent contrast, note that, this result may appear in contrast to the known convergence behaviour of internal coordinate values, since along the same eigenvector the actual internal coordinate value is restored the slowest, while converging to the critical point. The complete set of possible nuclear configurations of a molecule can never be a vector space, however, using the manifold theoretical approach consistent sets of local coordinate systems can be introduced. Accordingly, the theorem is first proven for a symmetry deficiency measure defined in terms of the metric of the reduced nuclear configuration space (manifold M of nuclear configurations), and then for a very general family of symmetry deficiency measures with bounds of finite degree polynomial dependence on nuclear configurations. Some implications of the role of the theorem in geometry optimizations are pointed out. † This paper is dedicated to Professor Michael A. Robb.

Three-Dimensional Structure of Neuropeptide K Bound to Dodecylphosphocholine Micelles

Neuropeptide K (NPK), an N-terminally extended form of neurokinin A (NKA), represents the most potent and longest lasting vasodepressor and cardiomodulatory tachykinin reported thus far. NPK has been shown to have high selectivity for the NK2 receptor. Because the micelle-associated structure may be relevant to the NPK-receptor interaction, the three-dimensional structure of the NPK in aqueous and micellar environments has been studied by two-dimensional proton nuclear magnetic resonance (2D (1)H NMR spectroscopy) and distance geometry calculations. Proton NMR assignments have been carried out with the aid of correlation spectroscopy (DQF-COSY and TOCSY) and nuclear Overhauser effect spectroscopy (NOESY and ROESY) experiments. The interproton distances and dihedral angle constraints obtained from the NMR data have been used in torsion angle dynamics algorithm for NMR applications (DYANA) to generate a family of structures, which have been refined using restrained energy minimization and dynamics. The results show that in an aqueous environment NPK lacks a definite secondary structure, although some turn-like elements are present in the N terminus. The structure is well-defined in the presence of dodecylphosphocholine micelles. The global fold of NPK bound to DPC micelles consists of two well-defined helices from residues 9 to 18 and residues 27 to 33 connected by a noncanonical beta turn. The N terminus of the peptide is characterized by a 3(10) helix or a series of dynamic beta turns. The conformational range of the peptide revealed by NMR and circular dichroism (CD) studies has been analyzed in terms of characteristic secondary features. The observed conformational features have been further compared to a NKA and neuropeptide gamma (NPgamma) potent endogenous agonist for the NK2 receptor.

Investigation of Herzberg–Teller Franck–Condon approaches and classical simulations to include effects due to vibronic coupling in circular dichroism spectra: The case of dimethyloxirane continued

AbstractA recent study has shown that the inclusion of vibrational effects may be vital in first‐principles simulations of circular dichroism (CD) spectra. In the present work, we show that effects from vibronic coupling or, alternatively, Herzberg–Teller corrections, can have additional and perhaps unusually strong effects, due to delicate cancellations between positive and negative contributions in a CD spectrum. As full vibronic coupling simulations tend to be too demanding computationally for the sizeable molecules considered in CD spectroscopy, it is pertinent to investigate suitable approximations. In the first part of this study, we examine various Herzberg–Teller Franck–Condon (HT–FC) approaches that include the geometrical dependence of the rotatory strength for a 3 × 3 linear vibronic model, for which exact numerical results are easily obtained. Somewhat disappointingly, none of the HT–FC approaches investigated here yielded sufficiently satisfactory results. In a subsequent part of this study, we show that purely classical simulations, based on a vibronic model, can provide reliable spectra and appear to be well suited to address the dependence of the rotatory strength on nuclear geometry. From the classical simulations we extract average rotatory strengths for each electronic state, which are then used in subsequent gradient FC calculations to incorporate vibrational fine structure in the CD spectrum. This mixed classical/gradient FC approach is applied to the methyloxirane CD spectrum, using the statistical averaging of (model) orbital potentials–time‐dependent density functional theory (SAOP–TDDFT) vibronic model presented recently and is shown to improve substantially on the original simulation, corroborating the potential importance of vibronic coupling effects in simulations of CD spectra. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

Extension of the active‐space equation‐of‐motion coupled‐cluster methods to radical systems: The EA‐EOMCCSDt and IP‐EOMCCSDt approaches

AbstractThe development of the active‐space variants of the electron‐attached (EA) and ionized (IP) equation‐of‐motion coupled‐cluster (EOMCC) methods, in which higher‐than‐doubly excited components of the cluster operator T and higher than 2p‐1h or 2h‐1p components of the electron attaching and ionizing operators R are defined through the use of active orbitals, is discussed. As shown by preliminary test calculations of adiabatic excitation energies and potential energy curves for the low‐lying states of the CH and OH radicals, the basic active‐space EA‐EOMCC and IP‐EOMCC methods, referred to as the EA‐EOMCCSDt and IP‐EOMCCSDt approaches, are capable of accuratelydescribing the ground and excited states of open‐shell systems, even at the moderately stretched nuclear geometries and even for states with a strong multi‐determinantal or doubly excited character, at the low costs that are on the order of those characterizing the standard EOMCC singles and doubles method. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

REMPI-TOF studies of the translational anisotropy and the polarization of the O (1D2) photofragment angular momentum following ozone photolysis at 298 nm

The translational anisotropy and the polarization of the electronic angular momentum of the O ((1)D2) fragment produced from the 298 nm photodissociation of ozone have been determined using resonance enhanced multiphoton ionization (REMPI) in conjunction with time-of-flight mass spectrometry (TOFMS). The translational anisotropy parameter beta, which is necessarily averaged over the O2 co-fragment rotational distribution, is measured to be 1.08 +/- 0.04. This is consistent with that expected for the (1)B2 <-- (1)A1 transition within an impulsive model if the tangential velocity associated with the zero point motion of the bend is constricted to opening the bond angle. Molecular frame polarization parameters of rank up to k = 4 have been extracted for the O ((1)D2) fragment and the calculated m(J) populations show a strong preference for the absolute value(m(J)) = 1 states. A small coherence term is also observed, a manifestation of the nuclear geometry of the dissociating molecule and the existence of possible non-adiabatic processes in the exit channel. The orientation associated with the mapping of the photon helicity onto the O ((1)D2) electronic angular momentum distribution was observed to have been quenched. However, the parameter gamma1', which describes the contribution to the orientation from a coherent superposition of a parallel and perpendicular excitation where the photofragment angular momentum lies perpendicular to both the recoil velocity and to the transition dipole moment, was determined to be -0.06.

Nuclear chromatin patterns in 3 glucocorticoid-resistant RPMI 8226 human myeloma cell sub-lines: Correlations with cell growth and immunological phenotype

Nuclear morphological alterations associated with glucocorticoid resistance in human myeloma were evaluated by image cytometry in 3 human myeloma RPMI 8226 cell sub-lines. Resistance was induced by drug selection using prednisone (8226p), methylprednisolone (8226m) and dexamethasone (8226d), respectively. All these 3 cell sublines displayed significant glucocorticoid-resistance without cross-resistance to doxorubicin. Nuclear geometry and texture were analyzed on G0/G1-selected cell nuclei and data compared with cell growth characteristics and membrane expression of CD23, CD38, CD44, and CD58 antigens. When compared to the parental RPMI 8226 cell line, glucocorticoid-resistant cells display a progressive chromatin condensation with heterogeneously distributed large chromatin clumps, a phenomenon not observed in the multidrug-resistant CEM-VLB cells. These alterations were correlated to the resistance index against glucocorticoids and to the expressions of CD38, and of CD44 variant forms CD44v5 and CD44v7-8 antigens. These data suggest that glucocorticoid resistance in RPMI 8226 cells could be associated with sub-visual specific higher-order chromatin organization changes. Furthermore, these alterations are correlated to the expression of membrane markers associated with tumors aggressiveness.

Theory of the photodissociation of ozone in the Hartley continuum: Potential energy surfaces, conical intersections, and photodissociation dynamics

Ab initio potential energy and transition dipole moment surfaces are presented for the five lowest singlet even symmetry electronic states of ozone. The surfaces are calculated using the complete active space self consistent field method followed by contracted multireference configuration interaction (MRCI) calculations. A slightly reduced augmented correlation consistent valence triple-zeta orbital basis set is used. The ground and excited state energies of the molecule have been computed at 9282 separate nuclear geometries. Cuts through the potential energy surfaces, which pass through the geometry of the minimum of the ground electronic state, show several closely avoided crossings. Close examination, and higher level calculations, very strongly suggests that some of these seemingly avoided crossings are in fact associated with non-symmetry related conical intersections. Diabatic potential energy and transition dipole moment surfaces are created from the computed ab initio adiabatic MRCI energies and transition dipole moments. The transition dipole moment connecting the ground electronic state to the diabatic B state surface is by far the strongest. Vibrational-rotational wavefunctions and energies are computed using the ground electronic state. The energy level separations compare well with experimentally determined values. The ground vibrational state wavefunction is then used, together with the diabatic B<--X transition dipole moment surface, to form an initial wavepacket. The analysis of the time-dependent quantum dynamics of this wavepacket provides the total and partial photodissociation cross sections for the system. Both the total absorption cross section and the predicted product quantum state distributions compare well with experimental observations. A discussion is also given as to how the observed alternation in product diatom rotational state populations might be explained.

Medium-induced jet absorption in relativistic heavy-ion collisions

The dense medium created in $\mathrm{Au}+\mathrm{Au}$ collisions at the Relativistic Heavy-Ion Collider significantly suppresses particle production from hard-scattering processes and their characteristic back-to-back angular correlation. We present a simple model of jet absorption in dense matter that incorporates a realistic nuclear geometry. Our calculations are performed at the jet level and assume independent jet fragmentation in the vacuum. This model describes quantitatively the centrality dependence of the observed suppression of the high ${p}_{T}$ hadron yield and of the back-to-back angular correlations. The azimuthal anisotropy of high ${p}_{T}$ particle production cannot be accounted for using a realistic nuclear geometry.

Quantum control of molecular motion including electronic polarization effects with a two-stage toolkit

A method for incorporating strong electric field polarization effects into optimal control calculations is presented. A Born-Oppenheimer-type separation, referred to as the electric-nuclear Born-Oppenheimer (ENBO) approximation, is introduced in which variations of both the nuclear geometry and the external electric field are assumed to be slow compared with the speed at which the electronic degrees of freedom respond to these changes. This assumption permits the generation of a potential energy surface that depends not only on the relative geometry of the nuclei but also on the electric field strength and on the orientation of the molecule with respect to the electric field. The range of validity of the ENBO approximation is discussed in the paper. A two-stage toolkit implementation is presented to incorporate the polarization effects and reduce the cost of the optimal control dynamics calculations. As an illustration of the method, it is applied to optimal control of vibrational excitation in a hydrogen molecule aligned along the field direction. Ab initio configuration interaction calculations with a large orbital basis set are used to compute the H-H interaction potential in the presence of the electric field. The significant computational cost reduction afforded by the toolkit implementation is demonstrated.

Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques

Little is known about how chromatin folds in its native state. Using optimized in situ hybridization and live imaging techniques have determined compaction ratios and fiber flexibility for interphase chromatin in budding yeast. Unlike previous studies, ours examines nonrepetitive chromatin at intervals short enough to be meaningful for yeast chromosomes and functional domains in higher eukaryotes. We reconcile high-resolution fluorescence in situ hybridization data from intervals of 14-100 kb along single chromatids with measurements of whole chromosome arms (122-623 kb in length), monitored in intact cells through the targeted binding of bacterial repressors fused to GFP derivatives. The results are interpreted with a flexible polymer model and suggest that interphase chromatin exists in a compact higher-order conformation with a persistence length of 170-220 nm and a mass density of approximately 110-150 bp/nm. These values are equivalent to 7-10 nucleosomes per 11-nm turn within a 30-nm-like fiber structure. Comparison of long and short chromatid arm measurements demonstrates that chromatin fiber extension is also influenced by nuclear geometry. The observation of this surprisingly compact chromatin structure for transcriptionally competent chromatin in living yeast cells suggests that the passage of RNA polymerase II requires a very transient unfolding of higher-order chromatin structure.

Deformation, nuclear motion and fragmentation of core-excited CO 2 probed by multiple-ion coincidence momentum imaging

The nuclear motion and geometry in core-excited CO 2 are probed using a multiple-ion-coincidence imaging technique. We demonstrate that CO 2 has a linear stable geometry in the C/O 1s −1 core-ionized state and a bent geometry in the C/O 1s −1π* core-excited state. The molecules in the C/O 1s −1π* A 1 and B 1 Renner–Teller states are probed to be bent in the A 1 state and linear in the B 1 state. The O O correlation angle distributions are well reproduced using a Coulomb explosion model which takes account of the zero point bending motion in the ground state, the classical bending motion along the potential energy curve of the core-excited state within the core-hole lifetime and the initial inhomogeneous charge distribution in the multiply charged molecular ion just before the dissociation. When the photon energy is tuned to be higher (lower) energy than the 1s −1π* resonance center, the events for the 1s −1π* A 1 states that result in the low O O correlation angle distribution are suppressed (enhanced).

Renormalized Coupled-Cluster Calculations of Reactive Potential Energy Surfaces: The BeFH System

The completely renormalized (CR) CCSD(T) method has been used to calculate the entire ground-state potential energy surface (PES) for the Be + HF reaction on a grid of nuclear geometries consisting of ∼3000 points. The cc-pVTZ and cc-pVQZ basis sets have been employed. In addition to the case of the Be atom approaching the HF molecule from the fluorine side and the case of the Be atom approaching HF from the hydrogen side, several values of the Be−F−H angle and the insertion of the Be atom between the H and F atoms of HF have been examined. The CR-CCSD(T) results have been compared with the results of CCSD(T) and multireference configuration interaction (MRCI) calculations. It has been demonstrated that the ground-state PES of the BeFH system obtained from the single-reference “black-box” CR-CCSD(T) calculations is in excellent agreement with the PES obtained from the expensive MRCI calculations, whereas the PES resulting from the standard CCSD(T) calculations is qualitatively incorrect and characterized ...