High-energy Structures Research Articles

Synthesis, characterization and conformational analysis of chloro-bis(glycylglycinate)germanium(iv) chloride

Chloro-bis(glycylglycinate)germanium(IV) chloride, [Cl(glygly)2Ge]Cl, was synthesized and characterized in the solid state by elemental analysis, thermogravimetry and infrared spectroscopy. Solution studies were also performed by 1H-NMR and 13C-NMR in dimethylsulfoxide (DMSO-d6) and by electric conductivity. The structural determination of the complex and the interpretation of the spectroscopic results were performed by employing an integrated computational approach, based on a systematic conformational search analysis on the [Cl(glygly)2Ge]+ ion performed by the Systematic Conformational Search Algorithm (SCSA) code, working at the hybrid B3LYP/6-31G(d,p) level. The combination of experimental and computational findings allowed us to draw the structure of the complex both in solid and in solution, showing the usefulness of the conformational search as well as the need to also take into account relatively high energy structures and secondary minima to obtain a clear picture of the title compound.

1SD-03 高圧力NMRから見る蛋白質の高エネルギー構造の世界(1SD タンパク質立体構造の揺らぎと生物機能の関連にNMR法は何処まで迫れるか?,日本生物物理学会第49回年会(2011年度))

1SD-03 高圧力NMRから見る蛋白質の高エネルギー構造の世界(1SD タンパク質立体構造の揺らぎと生物機能の関連にNMR法は何処まで迫れるか?,日本生物物理学会第49回年会(2011年度))

DFT versus Møller–Plesset conformational profile and vibrational assignments of non- planar phenoxyacetic acid and 2,3,4,5,6-pentafluorophenoxyacetic acid

The structural stability of phenoxyacetic acid and 2,3,4,5,6-pentafluorphenoxyacetic acid was investigated by the DFT-B3LYP and the ab initio MP2 calculations with the 6-311G ** basis set. For the parent acid the calculations were extended to the MP4(SDQ) level of theory. At the DFT-B3LYP level of calculation the planar Tttp ( transoid O C O H) was predicted to be about 0.5 and 1.3 kcal/mol lower in energy than the non-planar Cgcpp and Tgcpp ( cisoid O C O H) forms, respectively. At the MP2 and the MP4(SDQ) levels the Cgcpp form was predicted to be about 0.8 and 1.4 kcal/mol lower in energy than the Tgcpp and the Tttcp structures, respectively. On the basis of the Møller–Plesset calculations the Cgcpp and the Tgcpp conformations were adopted as the low and high energy structures of phenoxyacetic acid. The observed spectral intensities of phenoxyacetic acid were consistence with the Cgcpp conformation being the predominant form of the acid at room temperature. At the DFT and MP2 levels of theory 2,3,4,5,6-pentafluorophenoxyacetic acid was predicted to exist predominantly in the Cgcpp structure. The vibrational wavenumbers were computed at the B3LYP level of theory and tentative vibrational assignments were provided on the basis of combined theoretical and experimental infrared and Raman data of both molecules.

Unsaturation in trinuclear cobalt carbonyl compounds of the type ECo 3(CO) n (E = CH, CF, P, As; n = 9, 8, 7, 6) with Co 3E tetrahedrane structures

Theoretical studies on the known trinuclear cobalt carbonyl derivatives ECo 3(CO) 9 (E = CH, CF, P, As) predict structures with carbonyl groups bridging each edge of the Co 3 triangle in contrast with experiment where structures with all terminal carbonyl groups are found in all cases. However, the energy differences are predicted to be rather small ranging from 4 ± 2 kcal/mol for FCCo 3(CO) 9 to 10 ± 3 kcal/mol for AsCo 3(CO) 9. The global minima for the unsaturated ECo 3(CO) n ( n = 8, 7, 6) derivatives generally have two (for n = 8) or three (for n = 7 and 6) carbonyl groups bridging the edges of the Co 3 triangle. However, structures with all terminal carbonyl groups are also found in all cases as well as higher energy structures in which one of the carbonyl groups bridges all three cobalt atoms. The fluoromethinyl derivatives FCCo 3(CO) n ( n = 9, 8, 7) are anomalous since their unbridged structures or structures with a carbonyl group bridging all three cobalt atoms are closer in energy to the doubly or triply bridged global minima than is the case for the other ECo 3(CO) n derivatives.

Structures of Alkali Metal Ion−Adenine Complexes and Hydrated Complexes by IRMPD Spectroscopy and Electronic Structure Calculations

Complexes between adenine and the alkali metal ions Li(+), Na(+), K(+), and Cs(+) have been investigated by infrared multiple photon dissociation (IRMPD) spectroscopy between 2800 and 3900 cm(-1), as have some singly hydrated complexes. The IRMPD spectra clearly show the N-H stretching and the NH(2) symmetric and asymmetric stretching vibrations of adenine; and for the solvated ions, the O-H stretching vibrations are observed. These experimental spectra were compared with those for a variety of possible structures, including both A9 (A9 refers to the tautomer where hydrogen is on the nitrogen in position 9 of adenine, see Scheme 1) and A7 adenine tautomers, computed using B3-LYP/6-31+G(d,p). By comparing the experimental and the simulated spectra it is possible to rule out various structures and to further assign structures to the species probed in these experiments. Single-point calculations on the B3-LYP/6-31+G(d,p) geometries have been performed at MP2/6-311++G(2d, p) to obtain good estimates of the relative thermochemistries for the different structures. In all cases the computed IR spectrum for the lowest energy structure is consistent with the experimental IRMPD spectrum, but in some cases structural assignment cannot be confirmed based solely upon comparison with the experimental spectra so computed thermochemistries can be used to rule out high-energy structures. On the basis of the IRMPD spectra and the energy calculations, all adenine-M(+) and adenine-M(+)-H(2)O are concluded to be composed of the A7 tautomer of adenine, which is bound to the cations in a bidentate fashion through N3 and N9 (see Scheme 1 for numbering convention). For the hydrated ions water binds directly to the metal ion through oxygen, as would be expected since the metal contains most positive charge density. For the hydrated lithium cation-bound adenine dimer, the water molecule is concluded to be hydrogen bonded to a free basic site of one of the adenine monomers, which is also bound to the lithium cation. Experimental and theoretical results on adenine-Li(+)-H(2)O suggest that the electrosprayed adenine-Li(+) resembles the lowest-energy solution phase ion rather than the lowest-energy gas-phase ion, which is the imine form.

2SE1040 Volumetric Properties of Amyloid Fibrillation Starting from Unfolded High-Energy Protein Structures(2SE High-Energy Paradigm of Protein Structures,The 48th Annual Meeting of the Biophysical Society of Japan)

2SE1040 Volumetric Properties of Amyloid Fibrillation Starting from Unfolded High-Energy Protein Structures(2SE High-Energy Paradigm of Protein Structures,The 48th Annual Meeting of the Biophysical Society of Japan)

Rationalizing and functionalizing stannaspherene: Very stable stannaspherene “alloys”

It is illustrated here by ab initio calculations based on density functional theory and other high level methods that the high stability of the icosahedral Sn(12) (2-) dianion known as stannaspherene, reflects stability toward ionization rather than cohesion. This could be also connected with novel fluxional rearrangements and paths of Sn(12) (1-) leading eventually to Sn(12) (2-) involving charge transfer. In view of the very similar structural and electronic properties with the corresponding isovalent borane (B(12)H(12))(2-), it is demonstrated that stannaspherene can be further rationalized and functionalized on the basis of an isolobal analogy between group 14 clusters and isovalent boranes, carboranes, and bisboranes. Such analogy is of the same nature with analogous isolobal and isovalent similarities between silicon, hydrogenated silicon-carbon clusters and deltahedral boranes and carboranes, which the present author, scoptically and synoptically, has described as the "boron connection." It is predicted and verified theoretically: First, that the isovalent Bi(2)Sn(10) and Sb(2)Sn(10) clusters, considered as the microscopic analogs of tin-bismuth alloys, are very stable (more stable than stannaspherene itself) very symmetric and isolobal to Sn(12) (2-); and second, that embedded clusters of the form M@Sn(12) (2-), M@Bi(2)Sn(10), M=Pt,Pd are very stable and highly symmetrical (I(h) and D(5d) respectively) with large highest occupied-lowest unoccupied molecular orbital gaps and very large embedding energies of the order of 5-6 eV. It is furthermore predicted that Pt@Sn(12) (2-) and Pt@Bi(2)Sn(10) can be synthesized in view of their higher stability compared to Pt@Pb(12) (2-) which has already been synthesized. The marginal energy difference of 0.03 eV between the meta- and the para-isomer of Bi(2)Sn(10) indicates a fluxional behavior with respect to Bi-Sn interchange which should be related with the Sn(12) (1-) fluxionality leading eventually to Sn(12) (2-). This rearrangement is also associated with a strange aromatic behavior. The same type of Bi-Sn fluxionality is also encountered in higher energy structures. Due to the "inert pair effect" in tin, the validity of the isolobal analogy is much stronger and fully valid compared to isovalent species based on germanium or silicon, such as Ge(12) (2-), Bi(2)Ge(10), and Ge(10)C(2)H(2) and Si(12) (2-), Bi(2)Si(10), and Si(10)C(2)H(2). The present ideas are in full agreement with available experiments and suggest even further functionalization of stannaspherene, analogous to metaloboranes, metalocarboranes, and stannaboranes with several potential applications.

NMR spectroscopy brings invisible protein states into focus

Molecular dynamics are essential for protein function. In some cases these dynamics involve the interconversion between ground state, highly populated conformers and less populated higher energy structures ('excited states') that play critical roles in biochemical processes. Here we describe recent advances in NMR spectroscopy methods that enable studies of these otherwise invisible excited states at an atomic level and that help elucidate their important relation to function. We discuss a range of examples from molecular recognition, ligand binding, enzyme catalysis and protein folding that illustrate the role that motion plays in 'funneling' conformers along preferred pathways that facilitate their biological function.

Induced multiphoton adiabatic passage and coherent control of population transfer in quantum systems with high-energy transitions

A scheme for coherent population transfer via four quantum states in atomic or molecular systems of high-energy transitions by induced multiphoton adiabatic passage (IMAP) is proposed. The nonperturbative multiphoton resonant theory of interaction of such quantum systems with the two strong laser fields of different frequencies is developed and the possibility of coherent control of population in high-energy quantum structures by IMAP is shown.

Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations

We explore the effects of thermostats in replica exchange molecular dynamics (REMD) simulations. For thermostats that do not produce a canonical ensemble, REMD simulations are found to distort the configuration-space distributions. For bulk water, we find small deviations of the average potential energies, the buildup of tails in the potential energy distributions, and artificial correlations between the energies at different temperatures. If a solute is present, as in protein folding simulations, its conformational equilibrium can be altered. In REMD simulations of a helix-forming peptide with a weak-coupling (Berendsen) thermostat, we find that the folded state is overpopulated by about 10% at low temperatures, and underpopulated at high temperatures. As a consequence, the enthalpy of folding deviates by almost 3 kcal/mol from the correct value. The reason for this population shift is that non-canonical ensembles with narrowed potential energy fluctuations artificially bias toward replica exchanges between low-energy folded structures at the high temperature and high-energy unfolded structures at the low temperature. We conclude that REMD simulations should only be performed in conjunction with thermostats that produce a canonical ensemble.

Theoretical Study of Dispersion Binding of Hydrocarbon Molecules to Hydrogen-Terminated Silicon(100)-2×1

Noncovalent interactions between organic molecules and hydrogen-terminated silicon(100)-2×1 influence surface chemistry and diffusion. To develop our understanding of these interactions, we studied the dispersion binding of two model hydrocarbons, methane and benzene, on hydrogen-terminated silicon(100)-2×1 using a density-functional theory (DFT) technique incorporating dispersion corrections. The corrections were implemented using previously developed carbon-centered potentials (DiLabio, G. A. Chem. Phys. Lett. 2008, 455, 348−353.) and newly developed silicon-centered potentials, designed to correct the well-known erroneous long-range behavior of DFT methods. Our calculations predict that the preferred position for methane binding to the surface occurs over the area between two dimer rows (the “gulley”) and between two sets of dimers (binding energy (BE) = 2.2 kcal/mol). When the methane is positioned over a dimer row, BE = 1.9 kcal/mol. Diffusion of methane along the dimer row direction was calculated to be only marginally more facile than diffusion across rows. In the case of benzene, the preferred binding position is over the dimer row with the benzene roughly parallel to the surface and centered over one surface hydrogen (BE = 5.6 kcal/mol). The complex in which the benzene is over the gulley is less strongly bound (BE = 5.3 kcal/mol). Additional higher energy structures were also found. A detailed potential energy surface map reveals that diffusion of benzene in the row direction is more facile than diffusion across dimer rows. The calculated, room-temperature rate constant associated with diffusion along the row is calculated to be 1.7 times larger than that for diffusion in the perpendicular-to-row direction. Our findings show that surface anisotropy and molecule shape contribute to a directional preference for diffusion.

Infrared Multiple Photon Dissociation Spectra of Proton- and Sodium Ion-Bound Glycine Dimers in the N−H and O−H Stretching Region

The proton- and the sodium ion-bound glycine homodimers are studied by a combination of infrared multiple photon dissociation (IRMPD) spectroscopy in the N-H and O-H stretching region and electronic structure calculations. For the proton-bound glycine dimer, in the region above 3100 cm (-1), the present spectrum agrees well with one recorded previously. The present work also reveals a weak, broad absorption spanning the region from 2650 to 3300 cm (-1). This feature is assigned to the strongly hydrogen-bonded and anharmonic N-H and O-H stretching modes. As well, the shared proton stretch is observed at 2440 cm (-1). The IRMPD spectra for the proton-bound glycine dimer confirms that the lowest energy structure is an ion-dipole complex between N-protonated glycine and the carboxyl group of the second glycine. This spectrum also helps to eliminate the existence of any of the higher-energy structures considered. The IRMPD spectrum for the sodium ion-bound dimer is a much simpler spectrum consisting of three bands assigned to the O-H stretch and the asymmetric and symmetric NH 2 stretching modes. The positions of these bands are very similar to those observed for the proton-bound glycine dimer. Numerous structures were considered and the experimental spectrum agrees with the B3LYP/6-31+G(d,p) predicted spectrum for the lowest energy structure, two bidentate glycine molecules bound to Na (+). Though some of the structures cannot be completely ruled out by comparing the experimental and theoretical spectra, they are energetically disfavored by at least 20 kJ mol (-1).

Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states

Currently the main focus of structural biology is the determination of static three-dimensional representations of biomolecules that for the most part correspond to low energy (ground state) conformations. However, it is becoming increasingly well recognized that higher energy structures often play important roles in function as well. Because these conformers are populated to only low levels and are often only transiently formed their study is not amenable to many of the tools of structural biology. In this perspective we discuss the role of CPMG-based relaxation dispersion NMR spectroscopy in characterizing these low populated, invisible states. It is shown that robust methods for measuring both backbone chemical shifts and residual anisotropic interactions in the excited state are in place and that these data provide valuable restraints for structural studies of invisible conformers.

Dynamics of an anti-VEGF DNA aptamer: A single-molecule study

Single-molecule fluorescence resonance energy transfer (SMFRET) was used to study the interaction of a 25-nucleotide (nt) DNA aptamer with its binding target, vascular endothelial growth factor (VEGF). Conformational dynamics of the aptamer were studied in the absence of VEGF in order to characterize fluctuations in the unbound nucleic acid. SMFRET efficiency distributions showed that, while the aptamer favors a base-paired conformation, there are frequent conversions to higher energy conformations. Conversions to higher energy structures were also demonstrated to be dependent on the concentration of Mg 2+-counterion by an overall broadening of the SMFRET efficiency distribution at lower Mg 2+ concentration. Introduction of VEGF caused a distinct increase in the frequency of lower SMFRET efficiencies, indicating that favorable interaction of the DNA aptamer with its VEGF target directs aptamer structure towards a more open conformation.

Bonding of Seven Carbonyl Groups to a Single Metal Atom: Theoretical Study of M(CO)n (M = Ti, Zr, Hf; n = 7, 6, 5, 4)

The equilibrium geometries, thermochemistry, and vibrational frequencies of the homoleptic metal-carbonyls of the group 4 elements, M(CO)n (M = Ti, Zr, Hf; n = 7, 6, 5, 4) were predicted using density functional theory. Analogous M(CO)n structures were found for all three metals. The global minima for the 18-electron M(CO)7 molecules are all singlet C(3v) capped octahedra. The global minima for the 16-electron M(CO)6 species are triplet M(CO)6 structures distorted from O(h) symmetry to D(3d) symmetry. However, the corresponding singlet M(CO)6 structures lie within 5 kcal/mol of the triplet global minima. The global minima for M(CO)n (n = 5, 4) are triplet structures derived from the D(3d) distorted octahedral structures of M(CO)6 by removal of one or two CO groups, respectively. Quintet D(3h) trigonal bipyramidal structures for M(CO)5 and singlet T(d) tetrahedral structures for M(CO)4 are also found, as well as higher energy structures for M(CO)6 and M(CO)7 containing a unique CO group bonded to the metal atom through both M-C and M-O bonds. The dissociation energies M(CO)7 --> M(CO)6 + CO are substantial, indicating no fundamental problem in bonding seven CO groups to a single metal atom.

Modeling and analysis of disconnections in tilt walls

The transmission of dislocations through a pure tilt wall leaves a disconnection at the wall which has both step character and dislocation character. The relaxed configurations of the resulting high-energy dislocation structures are proposed and their long-range stress fields are studied both from a discrete dislocation perspective and also by representing them as equivalent disclination dipoles.

Structures, Rugged Energetic Landscapes, and Nanothermodynamics of Aln (2 ≤ n ≤ 65) Particles

Metal nanoparticles are important in several emerging technologies, but their size-selected thermodynamic properties are hard to obtain from experiment. We have characterized the energetic and structural properties of unsupported neutral Aln (2 <or= n <or= 65) particles (clusters and nanoparticles) via molecular dynamics quenching simulations with a recently validated many-body analytic potential. For each particle size (n), the global minimum-energy structure, the distribution of the local energy minima, and the finite-temperature thermodynamics have been calculated, the latter by evaluating approximately 100,000 rovibrational partition functions for the low-energy isomers of the various particles. This analysis demonstrates that the dominant structures of clusters and nanoparticles depend on temperature as well as particle size and that one must consider statistical mechanics as well as electronic structure in determining the dominant structures, stabilities, and properties of nanoparticles. As a particularly dramatic example, although the electronic magic numbers of Aln are n = 13, 19, 23, 38, and 55 when thermal energy is neglected, the n = 38 magic number is found to become unstable relative to its neighbors (n = 37 and 39) at temperatures of 500 K and above due to vibrational energy and entropy effects. Furthermore, an energy-landscape analysis based on the probability of finding an isomer demonstrates that for many particle sizes, the global-minimum-energy structure on the potential energy surface is not the dominant structure at moderate temperatures, and other low-energy isomers may be dominant at temperatures as low as room temperature. For example, the four lowest-energy structures account for less than 50% of the population for n = 17, 31, 33, 34, 36, 37, 39, 41-43, 50, 56, 58, and 63-65 at 300 K and for n = 10, 11, and 17-65 at 1500 K. At 1500 K, even the 64 lowest-energy structures account for less than half the population for n = 23, 27-55, and 57-65. The increased importance of higher-energy structures at finite temperatures has important implications for understanding the size-selective reactivity and catalytic activity of metal nanoparticles. The isomeric energy (EIso), which is the difference between the thermal average energy of the particle and that of the corresponding global minimum structure in the ground electronic state, is introduced as an indicator of how well the thermochemical properties of a multi-isomer particle can be represented by those of the global minimum structure. Particularly low values for Al12, Al13, Al19, Al48, Al53, Al54, and Al56 have been found in a wide temperature range.

Plastic deformation of orthoenstatite and the ortho- to high-pressure clinoenstatite transition: a metadynamics simulation study

Atomic-scale mechanisms of plastic deformation in orthoenstatite, MgSiO3 are studied by computer simulation methods. The combined use of metadynamics and molecular dynamics allows a direct observation of the structural changes during the creation of stacking faults in the (100) plane. A sequence of slip deformations in two different (100) planes at P = 15 GPa and T = 1,000 K reveals a probable transformation mechanism for the ortho- to high-pressure clinopyroxene transition. Each of the observed slips consists of at least four partial deformations crossing high-energy intermediate structures. In agreement with experimental studies, both (100)[010] and (100)[001] slip systems are activated in the deformation process. The observation of a dominant (100)[001] single slip system in pyroxenes may be related to the fact that high-energy intermediate dislocations with (100)[010] component are not stable on geological or experimental timescales.

A Shared Transcription Termination Signal on Negative and Ambisense RNA Genome Segments of Rift Valley Fever, Sandfly Fever Sicilian, and Toscana Viruses

The Phlebovirus genus (family Bunyaviridae) is composed of a diverse group of arboviruses that cause disease syndromes ranging from mild febrile illness to hemorrhagic fever with high fatality. Although antigenically similar, these viruses differ by approximately 25% at the genome level, and their ecologies, including geographic ranges, preferred vector species, and hosts, vary considerably. In contrast to other ambisense viruses, where RNA hairpin structures which serve as transcription termination signals are frequently found separating the opposite-sense open reading frames, no evidence of predicted high-energy hairpin structures was found at the ambisense junctions of phlebovirus S RNA segments. However, a conserved sequence motif was identified on both negative and ambisense genome segments that functions as a transcription termination signal for the N, NSs, and GPC mRNAs in three diverse phleboviruses, namely, Rift Valley fever, sandfly Sicilian, and Toscana viruses. The exact termination of nascent virus mRNA molecules was determined by 3' rapid amplification of cDNA ends. Surprisingly, analysis of the termini of mRNAs from both S and M segments of these three viruses revealed that transcription termination occurred immediately upstream of a conserved sequence motif with the general features 3'-C(1-3)GUCG/A-5'. In contrast, no corresponding sequence motif was found in the L segments, and analysis indicated a "runoff" transcript approach to L mRNA termination. The absolute requirement of the identified transcription termination motif was demonstrated by using a highly efficient Rift Valley fever virus reverse genetics system to generate live recombinant viruses with S segments lacking the termination signal motif for the NP or NSs mRNA and showing that these recombinant viruses generated mRNAs that failed to terminate correctly.

The ‘Evaporiti di Monte Castello’ deposits of the Messinian Southern Apennines foreland basin (Irpinia–Daunia Mountains, Southern Italy): stratigraphic evolution and geological context

Abstract An evaporitic limestone–gypsum succession, belonging to the Evaporiti di Monte Castello Formation, is recognized in the late Messinian (Upper Miocene) of the Irpinia–Daunia Mountains in the Southern Apennines arc (Southern Italy). This unit is formed by diatomaceous marls, massive and laminated evaporitic limestones, and by primary and clastic gypsum. Detailed stratigraphical, sedimentological and strontium geochemistry data has permitted reconstruction of stratigraphic and facies relations of gypsum deposits, depositional environment and basin evolution. Genetically related gypsum lithofacies can be grouped into two facies associations. The autochthonous gypsum facies association consists of shallow water selenitic, acicular and laminated gypsum and is characterized by the absence of high-energy sedimentary structures. The redeposited clastic gypsum facies association consists of shallow- to deeper-water fine-grained laminated gypsum, gypsarenites, pebbly gypsarenites and gypsrudites, showing common features of resedimented deposits. Nodular structures occurring in the laminated gypsum lithofacies seem to be mostly related to late diagenetic processes. The sedimentary evolution during the evaporative phase was characterized by a gradual increase in salinity until gypsum precipitated; then the sedimentary conditions in the basin were characterized by almost homogenous salinity conditions, and influenced by events of gypsum reworking and resedimentation probably related to flooding episodes and local tectonic activity. The gypsum was deposited from mainly marine brines, based on their Sr isotopic compositions. This sedimentary series is an equivalent of the Lower Evaporites of other parts of the Mediterranean. The Messinian Monte Castello Formation evaporites represent an uncommon type of evaporitic succession, probably developed in a extensional setting in a basin located along the Apulian foreland ramp, in contrast with the northern Apennines and Sicilian basins (e.g. Vena del Gesso, and Caltanisetta basins), which are considered to be thrust-top basins of the Apennine–Maghrebian foreland basin system.