T-shaped Conformation Research Articles

The Surprising Crystal Packing of Chlorinefluoride

The crystal structure of ClF was detd. at -188 Deg. ClF is monoclinic, space group P21/c, with a 6.378(1), b 4.247(1), c 6.425(1) .ANG., b 104.55(3) Deg; dc = 2.147,Z = 4, R = 0.0357, Rw = 0.0401 for 765 reflections. In the crystal individual ClF mols. form infinite planar ribbons along the screw axis, which are characterized by very short intermol. Cl...Cl contacts (3.070 .ANG.) between neighboring mols. An ab initio energy surface scan was performed for the ClF dimer by using the 6-311-G* basis set. Although the global energy min. of the ClF dimer was found for conformation A in the theor. study of the dimer, the T-shaped conformation (C,D) also has a min. which is energetically close to A, but is favored in the infinite ribbons of the crystal lattice. Some pos. charge is found in the prolongation of the F-Cl bond and some neg. charge perpendicular to the bond at the Cl atom, which holds the mols. together.

Calculation of the absorption spectrum of benzene in condensed phase. A study of the solvent effects

The red shift of the first absorption band of benzene in the condensed phase is calculated. The solid-phase calculations are performed using the experimental crystal structure. For the liquid two different approaches are considered. One is the herringbone structure suggested by X-ray experiments, and the other uses supermolecules generated by Monte Carlo simulation. Attention is given to the contribution of the usual parallel and T-shape conformations of the benzene dimers obtained in the simulation. Comparison with experiment shows a relatively poor result for the herringbone structure and good agreement for the supermolecular structures generated by the simulation. Q 1997 John Wiley & Sons, Inc. Int J Quant Chem 65: 885)891, 1997

(−)-Thebaine

The structure of the opioid thebaine (6,7,8,14-tetradehydro-4,5-epoxy-3,6-dimethoxy-17-methyl­morphinan), C19H21NO3, has been determined by single-crystal X-ray diffraction techniques at low temperature. The thebaine molecule adopts the same T-shaped conformation of the five fused rings as found in closely related rigid opioids. The geometry of the double bond at the bridgehead carbon atom is significantly distorted from planarity.

Visualization and comparison of molecular dynamics simulations of leukotriene C 4, leukotriene D 4, and leukotriene E 4

Molecular dynamics simulations of leukotriene C 4 (LTC 4), leukotriene D 4 (LTD 4), and leukotriene E 4 (LTE 4) were carried out, and the data were visualized in an animated video format. Three-dimensional ghost images show the positions of the heavy atoms of all three molecules throughout the simulations. The ghost images can be superimposed to give a single three-dimensional image in which the shapes of the most populated conformers of each molecule are apparent and can be compared. Leukotriene D 4 was found to occupy mostly T-shaped conformations, while LTC 4 occupied mostly cup-shaped conformations, and LTE 4 occupied a wide range of conformations spanning the LTD 4 and LTC 4 types. Digital filtering and graphing of the internal geometries of the molecules as a function of time revealed differences in dynamic behavior. The results are discussed in light of current knowledge about leukotriene receptors.

Theoretical Approaches to Molecular Magnetism II: No-Overlap and Orientation Principles for Ferromagnetic Interactions

Abstract No-overlap and orientation principles for ferromagnetic interactions between organic radicals were derived on the basis of approximately spin-projected UMP4(2) and UCC SD(T)/4-31G computations for several typical radical pairs. Ferromagnetic intermolecular interactions are feasible at T-shape and rhombus conformations in parallel interplane orientations for radical pairs because of no-overlap between π*-type SOMOs (no kinetic exchange) and nonzero-potential exchange via the SOMO-SOMO through-space contact, whereas antiferromagnetic kinetic exchange interactions are predominant at many other conformations.

No-overlap and orientation principle for ferromagnetic interactions between nitroxide groups

Approximately spin-projected UMP4(2) and UCC SD(T) computations show that ferromagnetic intermolecular interactions are feasible for T-shape and rhombus conformations in parallel interplane orientations for nitroxide pairs because of no-overlap between π ∗ -type SOMOs (no kinetic exchange) and non-zero potential exchange via SOMO-SOMO through-space contact. On the other hand, antiferromagnetic kinetic exchange interactions via SOMO-SOMO overlap are predominant for rectangular conformations. The no-overlap and orientation principle proposed previously is a useful guide for the theoretical understanding of ferromagnetic exchange interactions between nitroxide groups. Implications of the calculated results are discussed in relation to the discovery of ferromagnetic interactions in the crystals of adamantane dinitroxide, TEMPO derivatives and MOTMP.

Simplification of the transition state concept in reactive island theory: Application to the HCN⇄CNH isomerization

The reactive island (RI) theory of chemical reaction rates is modified so that a precise knowledge of the transition state is not required. This revised form of the theory is applied to a realistic two (J=0) and three degree of freedom model (J≠0) of the isomerization HCN⇄CNH. The detailed reaction dynamics is examined and understood in terms of the cylindrical manifolds embedded in the molecular phase space. Of special interest we find a T-shaped conformer in addition to the HCN and CNH moieties at J=0. Rates of unimolecular decay are examined by numerical simulation and theory. Good agreement is found between theory and simulation except for a case where a substantial amount of phase space is consumed by regular motion. In all cases studied, the theory is a significant improvement over the Rice–Ramsperger–Kassel–Marcus (RRKM) theory, which is up to three orders of magnitude too large.

The carbon dioxide dimer

Ab initio calculations with a large basis set (5s 4p 2d), including correlation by second-order Moller-Plesset perburbation theory (MP2), are performed for the dimer of carbon dioxide. The energies, structures and IR frequencies are all calculated at this level. It is found that the T-shaped conformation is a transition state between two slipped parallel dimers of such low energy that even at relatively low temperatures a planar geared motion is possible. (Similar behaviour has been found previously for the acetylene dimer.) The experimental data available are in excellent agreement with our results.

Terminal structure of a densovirus implies a hairpin transfer replication which is similar to the model for AAV

We cloned the complete sequence of Bombyx DNV (Ina isolate; Bm DNV-1) genome in a bacterial plasmid pUC 119 and determined the nucleotide sequences of both termini, resulting in elucidation of the nucleotide sequence of the complete genomic DNA of DNV. The complete sequence of the DNV DNA (5048 nucleotides) has inverted repeats of 225 nucleotides and the terminal 153 nucleotides are palindromic. The palindromes can fold back on themselves to form a hairpin structure but, unlike AAV, the small internal palindrome which forms a T-shaped conformation was not observed. End-label analysis demonstrated that the palindromic sequences at both termini can exist in either of two orientations (flip or flop) in virion DNA with different frequencies. These data suggest that the hairpin transfer model for AAV replication must be modified to explain the DNV replication. Additionally, a comparison study on the terminal structures of insect, human, and rodent parvoviruses allowed a prediction on the ancestral terminal structure of parvovirus genome.

Sequence and symmetry requirements within the internal palindromic sequences of the adeno-associated virus terminal repeat

The defective parvovirus, adeno-associated virus (AAV), contains a single-stranded DNA genome of 4681 bases with inverted terminal repeats of 145 bases. The distal 125 bases of the repeat are palindromic allowing a hairpin to form for initiation of DNA synthesis. The palindromic region contains three palindromes, two smaller internal palindromes flanked by a larger palindrome, which allow the hairpinned DNA to assume a T-shaped conformation during DNA replication. Deletion of an internal palindrome forming one of the crossarms of the T results in the inability of the AAV genome to be rescued from plasmid sequences and replicated. Restoration of the crossarm sequences with DNA that differs in primary sequence but maintains the symmetry of the palindrome results in viable AAV and propagation of the mutant sequences. In this paper we report further studies on the nature of mutants made within the crossarm of the T. Two types of substitution mutants were analyzed. Symmetrical sequence substitution mutants were viable as previously reported. An analysis of the kinetics of AAV DNA accumulation showed that the symmetrical sequence substitution mutants were indistinguishable from wild-type AAV. This was true if the AAV DNA was introduced into the cells either as plasmid DNA or as DNA extracted from virions. In contrast, intermolecular competition experiments showed either a dominance of the wild-type sequence or codominance of both sequences when both alleles were cotransfected into helper virus-infected cells. A preference for the wild-type sequence may also exist but is not required for efficient AAV replication. The second type of mutation studied was an asymmetrical sequence substitution mutant. This mutant was replicated but at a level too low to be propagated. These data suggest that symmetry is required in the internal palindromic region, presumably for the formation of the crossarm structure in the T-shape.

Study by X-ray diffraction of the geometrical shape of glycoprotein sugar chains in two model glycoconjugates, a liposaccharide and a phospholiposaccharide, having the same sugar chain

Two amphipatic, model glycoconjugates having the same sugar chain but differing in their hydrophobic component were studied by X-ray diffraction in concentrated water solution and in the dry state. The liposaccharide 2, obtained by linking the NH 2-4 group of the asparagine residue of the glycoaminoacid obtained from hen ovotransferrin with the activated carboxylic acid group of palmitic acid exhibited a cubic structure in which the sugar chain adopted a slightly deformed, “T-shaped conformation”. The phospholiposaccharide 3, obtained by linking the NH 2-4 group of the asparagine residue of the same glycoamino acid with the primary amine group of dipalmitoylphosphatidylethanolamine through a suberyl bridge exhibited a lamellar structure in which the sugar chain adopted a “Y-shaped conformation”. Thus, it was possible to induce a conformational change of the hen ovotransferrin sugar chain by changing the “hydrophobic residue” to which it is linked.