Changes In Torsion Angles Research Articles

Conformational Preference and Cis−Trans Isomerization of 4(R)-Substituted Proline Residues

We report here the conformational preference and prolyl cis-trans isomerization of 4(R)-substituted proline dipeptides, N-acetyl-N'-methylamides of 4(R)-hydroxy-L-proline and 4(R)-fluoro-L-proline (Ac-Hyp-NHMe and Ac-Flp-NHMe, respectively), studied at the HF/6-31+G(d), B3LYP/6-31+G(d), and B3LYP/6-311++G(d,p) levels of theory. The 4(R)-substitution by electron-withdrawing groups did not result in significant changes in backbone torsion angles as well as endocyclic torsion angles of the prolyl ring. However, the small changes in backbone torsion angles phi and psi and the decrease of bond lengths r(Cbeta-Cgamma) or r(Cgamma-Cdelta) appear to induce the increase of the relative stability of the trans up-puckered conformation and to alter the relative stabilities of transition states for prolyl cis-trans isomerization. Solvation free energies of local minima and transition states in chloroform and water were calculated using the conductor-like polarizable continuum model at the HF/6-31+G(d) level of theory. The population of trans up-puckered conformations increases in the order Ac-Pro-NHMe < Ac-Hyp-NHMe < Ac-Flp-NHMe in chloroform and water. The increase in population for trans up-puckered conformations in solution is attributed to the increase in population for the polyproline-II-like conformations with up puckering. The barriers DeltaGct++ to prolyl cis-to-trans isomerization for Ac-Hyp-NHMe and Ac-Flp-NHMe increase as the solvent polarity increases, as seen for Ac-Pro-NHMe. In particular, it was identified that the cis-trans isomerization proceeds through the clockwise rotation about the prolyl peptide bond for Ac-Hyp-NHMe and Ac-Flp-NHMe in chloroform and water, as seen for Ac-Pro-NHMe.

On Updating Torsion Angles of Molecular Conformations

A conformation of a molecule is defined by the relative positions of atoms and by the chirality of asymmetric atoms in the molecule. The three main representations for conformations of molecules are Cartesian coordinates, a distance geometry descriptor (which consists of a distance matrix and the signs of the volumes of quadruples of atoms), and internal coordinates. In biochemistry, conformational changes of a molecule are usually described in terms of internal coordinates. However, for many applications, such as molecular docking, the Cartesian coordinates of atoms are needed for computation. Although, for each conformational change, the Cartesian coordinates of atoms can be updated in linear time (which is optimal asymptotically), the constant factor becomes significant if a large number of updates are needed. Zhang and Kavraki (J. Chem. Inf. Comput. Sci. 2002, 42, 64-70) examined three methods: the simple rotations, the Denavit-Hartenberg local frames, and the atom-group local frames. On the basis of their implementations, they showed that the atom-group local frames are more efficient than the other two. In this paper, by expressing the torsion-angle change as a composition of translations and rotations, we observe that the simple rotations can be implemented in an efficient way by taking advantage of consecutive operations. Both quantitative and experimental comparisons show that the improved simple rotations, in which rotations are expressed in unit quaternions, are as efficient as the atom-group local frames and, thus, have the advantage of avoiding the need of precomputations of a set of local frames and transformations between them.

Hydrogen‐bonded turns in proteins: The case for a recount

Beta-turns are sites at which proteins change their overall chain direction, and they occur with high frequency in globular proteins. The Protein Data Bank has many instances of conformations that resemble beta-turns but lack the characteristic N-H(i) --> O=C(i - 3) hydrogen bond of an authentic beta-turn. Here, we identify potential hydrogen-bonded beta-turns in the coil library, a Web-accessible database utility comprised of all residues not in repetitive secondary structure, neither alpha-helix nor beta-sheet (http://www.roselab.jhu.edu/coil). In particular, candidate turns were identified as four-residue segments satisfying highly relaxed geometric criteria but lacking a strictly defined hydrogen bond. Such candidates were then subjected to a minimization protocol to determine whether slight changes in torsion angles are sufficient to shift the conformation into reference-quality geometry without deviating significantly from the original structure. This approach of applying constrained minimization to known structures reveals a substantial population of previously unidentified, stringently defined, hydrogen-bonded beta-turns. In particular, 33% of coil library residues were classified as beta-turns prior to minimization. After minimization, 45% of such residues could be classified as beta-turns, with another 8% in 3(10) helixes (which closely resemble type III beta-turns). Of the remaining coil library residues, 37% have backbone dihedral angles in left-handed polyproline II structure.

Ligand-Free and -Bound Structures of the Binding Protein (LivJ) of the Escherichia coli ABC Leucine/Isoleucine/Valine Transport System: Trajectory and Dynamics of the Interdomain Rotation and Ligand Specificity

The leucine/isoleucine/valine-binding protein (LIVBP or LivJ) serves as the primary high-affinity receptor of the Escherichia coli ABC-type transporter for the three aliphatic amino acids. The first structure of LIVBP determined previously without bound ligand showed a molecule comprised of two domains which are far apart and bisected by a wide open, solvent-accessible cleft. Here we report the crystal structures of another ligand-free state and three complexes with the aliphatic amino acids. In the present ligand-free structure, the two domains are farther apart. In the three very similar complex structures, the two domains are in close proximity, and each desolvated ligand is completely engulfed in the cleft and bound by both domains. The two different ligand-free structures, combined with those of the very similar ligand-bound structures, indicate the trajectory and backbone torsion angle changes of the hinges that accompany domain closure and play crucial functional roles. The amino acids are bound by polar and nonpolar interactions, occurring predominantly in one domain. Consistent with the protein specificity, the aliphatic side chains of the ligands lie in a hydrophobic pocket fully formed following domain or cleft closure. Comparison of the structures of LIVBP with several different binding proteins indicates no correlations between the magnitudes of the hinge-bending angles and the protein masses, the ligand sizes, or the number of segments connecting the two domains. Results of normal-mode analysis and molecular dynamics simulations are consistent with the trajectory and intrinsic flexibility of the interdomain hinges and the dominance of one domain in ligand binding in the open state.

Structures of nitroso- and nitroguanidine X-ray crystallography and computational analysis

The X-ray structures of solid nitroguanidine (ngoH):orthorhombic, Fdd2, a = 17.6181(14), b = 24.848(2), c = 3.5901(4) A, V = 1571.7(3) A3, Z = 16 and nitrosoguanidine (ngH); monoclinic, P 21/n, a = 3.64510(10), b = 11.746(2), c = 8.6483(14) A, β = 99.167(2)∘, V = 365.55(9) A3, Z = 4 have been determined utilizing single crystal X-ray diffraction methods. The results are compared with the most stable gaseous configurations derived from ab inito calculations. The lowest energy calculated configuration for the ligands and experimentally observed crystal structures are in excellent agreement. In the solid state, both the ngoH and ngH contain discrete molecules in their unit cells which are planar (within experimental error), in the diamine configurations and are structurally identical except for an oxygen atom. In solid ngH, two ligand molecules have four nitrogen atoms arranged in a plane such that they are suitable for coordination to a nickel ion (1.945, 2.064 A), when it is at the 1/2, 1/2, 1/2 unit-cell position giving the observed complex. As far as we are aware, this is the first instance in which a ligand crystal structure is essentially the same, with minor distance, angle and torsion angle changes, as the complex it forms and suggests some potentially unique properties and applications for this material.

Effect of pressure on the crystal structure of L-serine-I and the crystal structure of L-serine-II at 5.4 GPa

The crystal structure of L-serine has been determined at room temperature at pressures between 0.3 and 4.8 GPa. The structure of this phase (hereafter termed L-serine-I), which consists of the molecules in their zwitterionic tautomer, is orthorhombic, space group P212121. The least compressible cell dimension (c), corresponds to chains of head-to-tail NH...carboxylate hydrogen bonds. The most compressible direction is along b, and the pressure-induced distortion in this direction takes the form of closing up voids in the middle of R-type hydrogen-bonded ring motifs. This occurs by a change in the geometry of hydrogen-bonded chains connecting the hydroxyl groups of the -CH2OH side chains. These hydrogen bonds are the longest conventional hydrogen bonds in the system at ambient pressure, having an O...O separation of 2.918 (4) A and an O...O...O angle of 148.5 (2) degrees ; at 4.8 GPa these parameters are 2.781 (11) and 158.5 (7) degrees . Elsewhere in the structure one NH...O interaction reaches an N...O separation of 2.691 (13) A at 4.8 GPa. This is amongst the shortest of this type of interaction to have been observed in an amino acid crystal structure. Above 4.8 GPa the structure undergoes a single-crystal-to-single-crystal phase transition to a hitherto uncharacterized polymorph, which we designate L-serine-II. The OH...OH hydrogen-bonded chains of L-serine-I are replaced in L-serine-II by shorter OH...carboxyl interactions, which have an O...O separation of 2.62 (2) A. This phase transition occurs via a change from a gauche to an anti conformation of the OH group, and a change in the NCalphaCO torsion angle from -178.1 (2) degrees at 4.8 GPa to -156.3 (10) degrees at 5.4 GPa. Thus, the same topology appears in both crystal forms, which explains why it occurs from one single-crystal form to another. The transition to L-serine-II is also characterized by the closing-up of voids which occur in the centres of other R-type motifs elsewhere in the structure. There is a marked increase in CH...O hydrogen bonding in both phases relative to L-serine-I at ambient pressure.

Oscillation of spontaneously generated optical activity in (±)-1-( p-nitrobenzoyloxy)indane solutions: ‘serial S N2 reactions’ in aggregates supported by the crystal structure. Frozen S N2 transition states and enantioselective distortions

(±)-Indan-1-yl 4-nitrobenzoate upon dissolution in CH 2Cl 2, surprisingly displays optical activity-usually levorotation which swings to dextrorotation over several hours, and gradually vanishes. Its crystal structure (redetermined for this study) reveals an unusually close contact (1.471 Å) between the C 1 chiral centre in one molecule, and the oxygen atom at C 1 in a neighbouring molecule of the same ‘ R’ configuration. Corresponding changes in bond lengths and torsion angles indicate a set of frozen S N2 transition states. These interactions apparently persist in the aggregated solution, enabling a ’serial S N2‘ process which can invert the C 1 configurations in the (presumed) chiral aggregates. The selective distortion of the ‘ R’ enantiomer in the crystal, and the spontaneous generation of optical activity upon dissolution, indicate processes that are akin to a second order asymmetric transformation.

When and how do diaminocarbenes dimerize?

No example of a simple uncatalyzed dimerization of a diaminocarbene has been clearly established, so it is timely to ask what factors control the thermodynamics of this reaction, and what mechanisms are responsible for the observed dimerizations? In agreement with qualitative experimental observations, the dimerizations of simple five- and six-membered-ring diaminocarbenes are calculated to be 100 kJ mol(-1) less favorable than those of acyclic counterparts. This large difference is semiquantitatively accounted for by bond and torsional angle changes around the carbene centers. Carbenes such as (Et(2)N)(2)C are kinetically stable in THF at 25 degrees C in agreement with calculated energy barriers, but they rapidly dimerize in the presence of the corresponding formamidinium ion. This proton-catalyzed process is probably the most common mechanism for dimer formation, and involves formation of C-protonated dimers, which can be observed in suitable cases. The possibility of alkali-metal-promoted dimerization is raised, and circumstantial evidence for this is presented.

Polymorphism in [(polyamine)Co(NO 2) x]Y crystals caused by changes in torsional angles of the (amine)N–Co–N–O fragments ( x = 2, Y = NO 3−: x = 3, Y = 0)

Herein, we report the synthesis and characterization of a third polymorph of trans-[Co(2,3,2-tet)(NO 2) 2]NO 3, III, crystallizing in space group P 1 ¯ (No. 2) obtained during an attempt to reproduce the synthesis of a previously reported polymorph, I (for more details of polymorphs I and II, see Introduction and references cited therein). The cations of polymorphs I and II differ primarily by the angles that the planes of the two –NO 2 ligands make with one another; the former being considerably larger than that in II. Polymorph III resembles II in that the torsional angular differences between the trans-nitro ligands are also small, but differ notably from that in I. The structure of the compound [(5-Me-(dpt)Co(NO 2) 3], was determined also. The space group is P2 1/ n, with two molecules in the asymmetric unit, whose occupancies are 65% and 35% for molecules IVa and IVb, respectively. Again, the two differ by the torsional angles of the nitro ligands, specially two of them whose angular orientations are vastly different. Molecules IVa and IVb are compared with a previously obtained polymorph V of this same compound reported earlier. Once more, V is closely related in stereochemistry to IVb, but differs markedly from IVa in nitro torsional angles. In all cases, the Co(amine) fragments are closely super-imposable and the differences in nitro torsional angles are the result of the availability of several amine hydrogens of the basal plane with which to make intra-molecular hydrogen bonds. Clearly, these hydrogen bonds must be of very similar strength and the barriers to rotation of the –NO 2 ligands must have energies similar to the energetics of the hydrogen bonds causing the torsional motions.

How Much Backbone Motion in Ubiquitin Is Required To Account for Dipolar Coupling Data Measured in Multiple Alignment Media as Assessed by Independent Cross-Validation?

The magnitude of backbone internal motions in the small protein ubiquitin that needs to be invoked to account for dipolar coupling data measured in multiple alignment media is investigated using an intuitively straightforward approach. This involves simultaneous refinement of the coordinates (against NOE, torsion angle, and dipolar coupling restraints) and optimization of the magnitudes and orientations of the alignment tensors by means of torsion angle simulated annealing and Cartesian space minimization. We show that N-H dipolar couplings in 11 different alignment media and N-C', H(N)-C', and C alpha-C' dipolar coupling in two alignment media can be accounted for, at approximately the level of uncertainty in the experimental data, by a single structure representation. Extension to a two-member ensemble representation which provides the simplest description of anisotropic motions in the form of a two-site jump model (in which the overall calculated dipolar couplings are the averages of the calculated dipolar couplings of the individual ensemble members), results in modest, but significant, improvements in dipolar coupling R-factors for both the working set of couplings used in the refinement and for the free cross-validated set of C alpha-H alpha dipolar couplings recorded in two alignment media. Extensions to larger ensemble sizes do not result in any R-factor improvement for the cross-validated C alpha-H alpha dipolar couplings. With a few notable exceptions, the amplitudes of the anisotropic motions are small, with S(2)(jump) order parameters > or =0.8. Moreover, the structural impact of those few residues that do exhibit larger amplitude motions (S(2)(jump) ranging from 0.3 to 0.8) is minimal and can readily be accommodated by very small backbone atomic rms shifts (<0.5 A) because of compensatory changes in phi and psi backbone torsion angles. In addition, evidence for correlated motions of N-H bond vectors is observed. For most practical applications, however, refinement of NMR structures against dipolar couplings using a single structure representation is adequate and will not adversely impact coordinate accuracy within the limits of the NMR method.

In situ high pressure phase transition of alcohol intercalated zirconium phosphate observed by synchrotron X-ray scattering

Measurements made on the SAXS beamline at Sincrotrone Elettra in Trieste indicated that a phase transition in which the alkanol chains undergo a change from an all trans-conformation to a conformation in which the O–C 1–C 2–C 3 torsion angle changes from 180 to 136° could be induced by a pressure change. p– T phase diagrams of 1-octanol, 1-nonanol, and 1-decanol intercalated alpha zirconium hydrogenphosphate were constructed. From them, the existence of both phases with different basal spacings is obvious. It can be deduced from the comparison of the data for the 1-octanol and 1-nonanol intercalates that the pressure at which this transition occurs, decreases with increasing length of the alkanol chain.

Distortion of the three-dimensional structure of the vnd/NK-2 homeodomain bound to DNA induced by an embryonically lethal A35T point mutation.

The three-dimensional solution structure obtained by NMR of the A35T mutant vnd/NK-2 homeodomain bound to the vnd/NK-2 consensus 16 bp DNA sequence was determined. This mutation to threonine from alanine in position 35 in helix II of the vnd/NK-2 homeodomain is associated with early embryonic lethality in Drosophila melanogaster. Although the unbound mutant protein is not structured, in the DNA-bound state it adopts the three-helix fold characteristic of all known homeodomains, but with alterations relative to the structure of the wild-type analogue. These structural modifications occur, and are accompanied by a 50-fold reduction in the DNA binding affinity, even though most of the protein-DNA interactions originally seen for the wild-type homeodomain are found likewise in the threonine analogue. Alterations include torsional angle changes in the loop between helix I and helix II, and in the turn between helix II and helix III, as well as in a distortion of the usual antiparallel orientation of helix I with respect to helix II. The alteration of the position of leucine 40 in the A35T mutant is proposed to explain the observed 1.27 ppm upfield shift of the corresponding amide proton resonance relative to the value observed for the wild-type analogue. A detailed comparison of the structures of the mutant A35T and wild-type vnd/NK-2 homeodomains bound to the cognate DNA is presented. The consequences of the structural alteration of the DNA-bound A35T mutant vnd/NK-2 protein may constitute the basis of the observed early embryonic lethality.

Membrane Protein Dynamics versus Environment: Simulations of OmpA in a Micelle and in a Bilayer

The bacterial outer membrane protein OmpA is one of the few membrane proteins whose structure has been solved both by X-ray crystallography and by NMR. Crystals were obtained in the presence of detergent, and the NMR structure is of the protein in a detergent micelle. We have used 10 ns duration molecular dynamics simulations to compare the behaviour of OmpA in a detergent micelle and in a phospholipid bilayer. The dynamic fluctuations of the protein structure seem to be ca 1.5 times greater in the micelle environment than in the lipid bilayer. There are subtle differences between the nature of OmpA–detergent and OmpA–lipid interactions. As a consequence of the enhanced flexibility of the OmpA protein in the micellar environment, side-chain torsion angle changes are such as to lead to formation of a continuous pore through the centre of the OmpA molecule. This may explain the experimentally observed channel formation by OmpA.

Structural specificity of heparin binding in the fibroblast growth factor family of proteins.

Heparin and heparan sulfate glycosaminoglycans (HSGAGs) mediate a wide variety of complex biological processes by specifically binding proteins and modulating their biological activity. One of the best studied model systems for protein-HSGAG interactions is the fibroblast growth factor (FGF) family of molecules, and recent observations have demonstrated that the specificity of a given FGF ligand binding to its cognate receptor (FGFR) is mediated by distinct tissue-specific HSGAG sequences. Although it has been known that sulfate and carboxylate groups in the HSGAG chain play a key role by interacting with basic residues on the proteins, there is little understanding of how these ionic interactions provide the necessary specificity for protein binding. In this study, using all of the available crystal structures of different FGFs and FGF-HSGAG complexes, we show that in addition to the ionic interactions, optimal van der Waals contact between the HSGAG oligosaccharide and the protein is also very important in influencing the specificity of FGF-HSGAG interactions. Although the overall helical structure is maintained in the FGF-bound HSGAG compared with unbound HSGAG, we observe distinct changes in the backbone torsion angles of the oligosaccharide chain induced upon protein binding. These changes result in local deviations in the helical axis that provide optimal ionic and van der Waals contact with the protein. A specific conformation and topological arrangement of the HSGAG-binding loops of FGF, on the other hand, impose structural constraints that induce the local deviations in the HSGAG structure, thereby enabling maximum contact between HSGAG and the protein.

Efficient Generation of Feasible Pathways for Protein Conformational Transitions

We develop a computationally efficient method to simulate the transition of a protein between two conformations. Our method is based on a coarse-grained elastic network model in which distances between spatially proximal amino acids are interpolated between the values specified by the two end conformations. The computational speed of this method depends strongly on the choice of cutoff distance used to define interactions as measured by the density of entries of the constant linking/contact matrix. To circumvent this problem we introduce the concept of using a cutoff based on a maximum number of nearest neighbors. This generates linking matrices that are both sparse and uniform, hence allowing for efficient computations that are independent of the arbitrariness of cutoff distance choices. Simulation results demonstrate that the method developed here reliably generates feasible intermediate conformations, because our method observes steric constraints and produces monotonic changes in virtual bond and torsion angles. Applications are readily made to large proteins, and we demonstrate our method on lactate dehydrogenase, citrate synthase, and lactoferrin. We also illustrate how this framework can be used to complement experimental techniques that partially observe protein motions.

Can the stereochemical outcome of glycosylation reactions be controlled by the conformational preferences of the glycosyl donor?

Previous static and dynamical density functional theory studies of the 2,6-di- O-acetyl-3,4- O-isopropylidene- d-galactopyranosyl cations and their methanol adducts has led to an hypothesis that these cations exist in two families of conformers characterized as 2 S O and B 2,5, respectively. These families differ by ring inversion, each with its own reactivity. New calculations on the 2,6-di- O-acetyl-3,4-di- O-methyl- d-galactopyranosyl cation confirmed these trends. Removing the isopropylidene group allows more flexibility, but two families of conformers can be discerned with the monocyclic oxocarbenium ions in the E 3 conformation and the bicyclic dioxolenium ions in the 4 H 5 conformation. Attack on the β-face of these monocyclic cations is favored by hydrogen bonding and the anomeric effect. The experimentally observed high β-stereoselectivity of mannopyranosyl donors and high α-stereoselectivity of glucopyranosyl donors with the 4,6- O-benzylidene protecting groups can be rationalized assuming that the trans-fused 1,3-dioxane ring allows population of only one family of conformers. The combination of hydrogen bonding and conformational changes of the pyranose ring in response to the C-5O-5C-1C-2 torsion angle changes are identified as key factors in stereoselectivity. Based on these observations a strategy to design face discriminated glycosyl donors that exist predominantly in only one family of conformers is proposed.

Electronic Properties and Conformation Analysis of π-Conjugated Distyryl Benzene Derivaties

A quantum-chemical investigation on the conformations and electronic properties of bis[2-{2-methoxy-4,6-di(t-butyl)phenyl}ethenyl]benzenes (MBPBs) as building block for <TEX>${\pi}$</TEX>-conjugate polymer are performed in order to display the effects of t-butyl and methoxy group substitution and of kink(ortho and meta) linkage. The conjugation length of the polymers can be controlled by substituents and kink linkages of backbone. Structures for the molecules, o-, m-, and p-MBPBs as well as unsubstituted o-, m-, and p-DSBs were fully optimized by using semiempirical AM1, PM3 methods, and ab initio HF method with 3-21G(d) basis set. The potential energy curves with respect to the change of single torsion angle are obtained by using semiempirical methods and ab initio HF/3-21G(d) basis set. The curves are similar shape in the molecules with respect to the position of vinylene groups. It is shown that the conformations of the molecules are compromised between the steric repulsion interaction and the degree of the conjugation. Electronic properties of the molecules were obtained by applying the optimized structures and geometries to the ZINDO/S method. ZINDO/S analysis performed on the geometries obtained by AM1 method and HF/3-21G(d) level is reported. The absorption wavelength on the geometries obtained by AM1 method is much longer than that by HF/3-21G(d) level. The absorption wavelength of MBPBs are red shifted with comparison to that of corresponding DSBs in the same torsion angle because of electron donating substituents. The absorption wavelength of isomers with kink(orth and meta) linkage is shorter than that of para linkage.

Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs

A series of DNA 21-mers containing a variety of the 4 × 4 internal loop sequence 5′-CAAG-3′/3′-ACGT-5′ were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG)/molecular dynamics (MD) approaches. Such oligomers exhibit excellent resolution in the NMR spectra and reveal many unusual NOEs (nuclear Overhauser effect) that allow for the detailed characterization of a DNA hairpin incorporating a track of four different non-Watson-Crick base-pairs in the stem. These include a wobble C·A base-pair, a sheared A·C base-pair, a sheared A·G base-pair, and a wobble G·T base-pair. Significantly different twisting angles were observed between the base-pairs in internal loop that results with excellent intra-strand and inter-strand base stacking within the four consecutive mismatches and the surrounding canonical base-pairs. This explains why it melts at 52°C even though five out of ten base-pairs in the stem adopt non-Watson-Crick pairs. However, the 4 × 4 internal loop still fits into a B-DNA double helix very well without significant change in the backbone torsion angles; only ζ torsion angles between the tandem sheared base-pairs are changed to a great extent from the gauche− domain to the trans domain to accommodate the cross-strand base stacking in the internal loop. The observation that several consecutive non-canonical base-pairs can stably co-exist with Watson-Crick base-pairs greatly increases the limited repertoire of irregular DNA folds and reveals the possibility for unusual structural formation in the functionally important genomic regions that have potential to become single-stranded.

Crystal Structure of (NH4)4H2(SeO4)3 and (ND4)4D2(SeO4)3 below 180 K

The structure of (NH4)4H2(SeO4)3 and (ND4)4D2(SeO4)3 superionic crystals below 180 K determined by X-ray single-crystal analysis is presented. The compounds have the following crystal data: (NH4)4H2(SeO4)3 (T=140 K), triclinic, space group P-1, a=7.647(2) Å, b=10.342(2) Å, c=10.558(2) Å, α=114.41(3)°, β=93.22(3)°, γ=107.47(3)°, V=709.4(3) Å3, Z=2, R=0.0358; (ND4)4D2(SeO4)3 (T=135 K), triclinic, space group P-1, a=7.660(2) Å, b=10.345(2) Å, c=10.552(2) Å, α=114.40(3)°, β=93.27(3)°, γ=107.50(3)°, V=710.3(3) Å3, Z=2, R1=0.0325. The two “acid” protons are involved in short hydrogen bonds of length ∼2.5 Å linking three SeO4 tetrahedra into a trimer. The dihydrogen triselenate anions are linked with the ammonium cations by weak H bonds (2.8–3.1 Å). No drastic changes in bond lengths within SeO4 tetrahedra were observed between room temperature and ∼140 K. The tendency to the N–H(D)…O bond network contraction can be related to slowing the ammonium ions's rotation. The mutual reorientation of SeO4 tetrahedra in trimers evidenced by torsion angle changes is negligible in the studied temperature range. The obtained results are compared with those previously reported and the reasons are given that at low temperatures both crystals preserve room temperature, nonpolar P-1 space group.

Electronic Spectroscopy of Jet-Cooled 1,2‘-Binaphthyl

The electronic spectroscopy of jet-cooled 1,2‘-binaphthyl has been examined by laser-induced fluorescence spectroscopy. Many medium length progressions were observed in two active vibrations with frequencies νA‘ = 35.1 cm-1 and νB‘ = 53.5 cm-1 assigned as the torsion and out-of-plane wag between the two naphthalene moieties, respectively. Two other low-frequency vibrations were measured: νC‘ = 60.6 cm-1 and νD‘ = 138.1 cm-1. These are also likely to involve inter-ring motion, possibly an in-plane wag for νC and an antisymmetric inter-ring motion for νD, although a low-frequency naphthalene ring vibration is also possible. The electronic origin transition was not observed because of a very weak Franck−Condon factor with the ground state. However, a Franck−Condon analysis provided an estimate of the origin transition at T00 = 30 828.2 cm-1. Progressions in both νA and νB are harmonic up to 13 quanta for νA and 5 quanta for νB. Therefore, the barrier for interconversion between the cis and trans conformers of 1,2‘-binaphthyl must be much higher than the 500 cm-1 of harmonic vibrations measured here. A diffuse band, about 800 cm-1 higher in energy, was assigned to the S2 ← S0 transition. Previous semiempirical calculations predicted the electronic energy of the S1 state and the magnitude of the naphthalene dimer splitting quite well. However, the calculations placed the interconversion barrier through 90° to be as low as 300 cm-1. The Franck−Condon analysis also provided a change in equilibrium conformation angle of 18° upon electronic excitation, again in disagreement with calculations, which predict essentially no change in equilibrium torsional angle between the S0, S1, and S2 states.