Showing papers on "Dihedral angle published in 2003"

VADAR: a web server for quantitative evaluation of protein structure quality

Abstract: VADAR (Volume Area Dihedral Angle Reporter) is a comprehensive web server for quantitative protein structure evaluation. It accepts Protein Data Bank (PDB) formatted files or PDB accession numbers as input and calculates, identifies, graphs, reports and/or evaluates a large number (>30) of key structural parameters both for individual residues and for the entire protein. These include excluded volume, accessible surface area, backbone and side chain dihedral angles, secondary structure, hydrogen bonding partners, hydrogen bond energies, steric quality, solvation free energy as well as local and overall fold quality. These derived parameters can be used to rapidly identify both general and residue-specific problems within newly determined protein structures. The VADAR web server is freely accessible at http://redpoll.pharmacy.ualberta.ca/vadar.

Refinement of protein structures in explicit solvent.

Abstract: We present a CPU efficient protocol for refinement of protein structures in a thin layer of explicit solvent and energy parameters with completely revised dihedral angle terms. Our approach is suitable for protein structures determined by theoretical (e.g., homology modeling or threading) or experimental methods (e.g., NMR). In contrast to other recently proposed refinement protocols, we put a strong emphasis on consistency with widely accepted covalent parameters and computational efficiency. We illustrate the method for NMR structure calculations of three proteins: interleukin-4, ubiquitin, and crambin. We show a comparison of their structure ensembles before and after refinement in water with and without a force field energy term for the dihedral angles; crambin was also refined in DMSO. Our results demonstrate the significant improvement of structure quality by a short refinement in a thin layer of solvent. Further, they show that a dihedral angle energy term in the force field is beneficial for structure calculation and refinement. We discuss the optimal weight for the energy constant for the backbone angle omega and include an extensive discussion of meaning and relevance of the calculated validation criteria, in particular root mean square Z scores for covalent parameters such as bond lengths.

Cyclic coordinate descent: A robotics algorithm for protein loop closure.

Abstract: In protein structure prediction, it is often the case that a protein segment must be adjusted to connect two fixed segments. This occurs during loop structure prediction in homology modeling as well as in ab initio structure prediction. Several algorithms for this purpose are based on the inverse Jacobian of the distance constraints with respect to dihedral angle degrees of freedom. These algorithms are sometimes unstable and fail to converge. We present an algorithm developed originally for inverse kinematics applications in robotics. In robotics, an end effector in the form of a robot hand must reach for an object in space by altering adjustable joint angles and arm lengths. In loop prediction, dihedral angles must be adjusted to move the C-terminal residue of a segment to superimpose on a fixed anchor residue in the protein structure. The algorithm, referred to as cyclic coordinate descent or CCD, involves adjusting one dihedral angle at a time to minimize the sum of the squared distances between three backbone atoms of the moving C-terminal anchor and the corresponding atoms in the fixed C-terminal anchor. The result is an equation in one variable for the proposed change in each dihedral. The algorithm proceeds iteratively through all of the adjustable dihedral angles from the N-terminal to the C-terminal end of the loop. CCD is suitable as a component of loop prediction methods that generate large numbers of trial structures. It succeeds in closing loops in a large test set 99.79% of the time, and fails occasionally only for short, highly extended loops. It is very fast, closing loops of length 8 in 0.037 sec on average.

Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts.

Abstract: A computer program (SHIFTX) is described which rapidly and accurately calculates the diamagnetic 1H, 13C and 15N chemical shifts of both backbone and sidechain atoms in proteins. The program uses a hybrid predictive approach that employs pre-calculated, empirically derived chemical shift hypersurfaces in combination with classical or semi-classical equations (for ring current, electric field, hydrogen bond and solvent effects) to calculate 1H, 13C and 15N chemical shifts from atomic coordinates. The chemical shift hypersurfaces capture dihedral angle, sidechain orientation, secondary structure and nearest neighbor effects that cannot easily be translated to analytical formulae or predicted via classical means. The chemical shift hypersurfaces were generated using a database of IUPAC-referenced protein chemical shifts – RefDB (Zhang et al., 2003), and a corresponding set of high resolution (<2.1 A) X-ray structures. Data mining techniques were used to extract the largest pairwise contributors (from a list of ∼20 derived geometric, sequential and structural parameters) to generate the necessary hypersurfaces. SHIFTX is rapid (< 1 CPU second for a complete shift calculation of 100 residues) and accurate. Overall, the program was able to attain a correlation coefficient (r) between observed and calculated shifts of 0.911 (1Hα), 0.980 (13Cα), 0.996 (13Cβ), 0.863 (13CO), 0.909 (15N), 0.741 (1HN), and 0.907 (sidechain 1H) with RMS errors of 0.23, 0.98, 1.10, 1.16, 2.43, 0.49, and 0.30 ppm, respectively on test data sets. We further show that the agreement between observed and SHIFTX calculated chemical shifts can be an extremely sensitive measure of the quality of protein structures. Our results suggest that if NMR-derived structures could be refined using heteronuclear chemical shifts calculated by SHIFTX, their precision could approach that of the highest resolution X-ray structures. SHIFTX is freely available as a web server at http://redpoll.pharmacy.ualberta.ca.

Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy.

Abstract: NMR measurements of a large set of protein backbone one-bond dipolar couplings have been carried out to refine the structure of the third IgG-binding domain of Protein G (GB3), previously solved by X-ray crystallography at a resolution of 1.1 A. Besides the commonly used bicelle, poly(ethylene glycol), and filamentous phage liquid crystalline media, dipolar couplings were also measured when the protein was aligned inside either positively or negatively charged stretched acrylamide gels. Refinement of the GB3 crystal structure against the 13Cα−13C‘ and 13C‘−15N dipolar couplings improves the agreement between experimental and predicted 15N−1HN as well as 13Cα−1Hα dipolar couplings. Evaluation of the peptide bond N−H orientations shows a weak anticorrelation between the deviation of the peptide bond torsion angle ω from 180° and the angle between the N−H vector and the C‘−N−Cα plane. The slope of this correlation is −1, indicating that, on average, pyramidalization of the peptide N contributes to small devi...

Force field influence on the observation of π-helical protein structures in molecular dynamics simulations

Abstract: In this study, we have investigated the sampling of π-helical conformations, with i, i + 5 hydrogen bonding, using empirical force fields. From replica exchange molecular dynamics simulations of the helical peptide acetyl-(AAQAA)3-amide using the CHARMM22 force field and implicit solvent, we find rapid conversion from an initial α-helix to π-helical conformations. While this confirms similar studies of different peptides in explicit solvent, it does not agree with experimental data where π-helices are rarely observed. The sampling of π-helices is significantly diminished in favor of canonical α-helices when a newly extended CHARMM22/CMAP force field is used, where the backbone dihedral φ/ψ potential map in a vacuum is matched exactly to high-level quantum mechanical data for an alanine dipeptide model system. Energetic analysis shows that the difference between α- and π-helical conformations of the alanine dipeptide in a vacuum is 2.6 kcal/mol according to quantum mechanical calculations while both confor...

Effects of ligand planarity on the interaction of polypyridyl Ru(II) complexes with DNA

Abstract: Two new polypyridyl ligands containing substituent Br at different positions in the phenyl ring, OBIP {OBIP = 2-(2-bromophenyl)imidazo[4,5-f]-1,10-phenanthroline}, PBIP {PBIP = 2-(4-bromophenyl)imidazo[4,5-f]-1,10-phenanthroline} and their Ru(II) complexes, [Ru(dmp)2(OBIP)]2+1 and [Ru(dmp)2(PBIP)]2+2 (dmp = 2,9-dimethyl-1,10-phenanthroline), have been synthesized and characterized. The binding of the two complexes to calf thymus DNA (CT DNA) has been investigated by spectrophotometric methods, viscosity measurements, as well as equilibrium dialysis and circular dichroism spectroscopy. Theoretical calculations for the two complexes were also carried out applying the density functional theory (DFT) method. The structure of complex 1 has been determined by single-crystal X-ray diffraction techniques. The imidazo[4,5-f]-1,10-phenanthroline moiety is not coplanar with the 2-bromophenyl ring, having a dihedral angle of 48.6° in the OBIP ligand. The twisted conformation has been further confirmed by theoretical calculations, in which this dihedral angle is 48.2°. The theoretical calculations also suggest that the PBIP ligand in complex 2 is essentially planar (dihedral angle is 0.4°). The experimental results show that while complex 1 binds to CT DNA via a semi-intercalative mode, complex 2 strongly binds to CT DNA through intercalation. Complex 2 is thus a much better candidate as an enantioselective binder to CT DNA than complex 1. Some experimental regularities or trends have been reasonably explained by the theoretical results. These suggest that the planarity of the intercalated ligand has significant effects on the spectral properties and the DNA-binding behavior of the complexes, and that the DFT method can be used effectively to explain and predict some regularities or trends in the interaction of polypyridyl Ru(II) complexes with DNA.

Insights into the mobility of methyl-bearing side chains in proteins from 3JCC and 3JCN couplings

Abstract: Side-chain dynamics in proteins can be characterized by the NMR measurement of 13C and 2H relaxation rates. Evaluation of the corresponding spectral densities limits the slowest motions that can be studied quantitatively to the time scale on which the overall molecular tumbling takes place. A different measure for the degree of side-chain order about the Cα−Cβ bond (χ1 angle) can be derived from 3JC‘-Cγ and 3JN-Cγ couplings. These couplings can be measured at high accuracy, in particular for Thr, Ile, and Val residues. In conjunction with the known backbone structures of ubiquitin and the third IgG-binding domain of protein G, and an extensive set of 13C−1H side-chain dipolar coupling measurements in oriented media, these 3J couplings were used to parametrize empirical Karplus relationships for 3JC‘-Cγ and 3JN-Cγ. These Karplus curves agree well with results from DFT calculations, including an unusual phase shift, which causes the maximum 3JCC and 3JCN couplings to occur for dihedral angles slightly small...

Oxidative Cleavage of DNA by a New Ferromagnetic Linear Trinuclear Copper(II) Complex in the Presence of H2O2/Sodium Ascorbate

Abstract: A new trinuclear copper(II) complex has been synthesized and structurally characterized: [Cu3(L)2(HCOO)2(OH)2]∞ (HL = (N-pyrid-2-ylmethyl)benzenesulfonylamide). In the complex, the central copper ion is six-coordinated. The coordination spheres of the terminal copper atoms are square pyramidal, the apical positions being occupied by a sulfonamido oxygen of the contiguous trimer. As a consequence, the complex can be considered a chain of trinuclear species. The three copper atoms are in a strict linear arrangement, and adjacent coppers are connected by a hydroxo bridge and a bidentate syn−syn carboxylato group. The mixed bridging by a hydroxide oxygen atom and a bidentate formato group leads to a noncoplanarity of the adjacent basal coordination planes with a dihedral angle of 61.4(2)°. Susceptibility measurements (2−300 K) reveal a strong ferromagnetic coupling, J = 79 cm-1, leading to a quartet ground state that is confirmed by the EPR spectrum. The ferromagnetic coupling arises from the countercompleme...

Probes for Narcotic Receptor Mediated Phenomena

Abstract: The synthesis of a series of epoxy 5-phenylmorphans is being explored in order to determine the conformational requirements of the phenolic ring in a phenylmorphan molecule that may be needed both for binding to a specific opioid receptor and for exhibiting opioid agonist or antagonist activity. Of the twelve possible ortho- and para-bridged isomers (a–f) (Fig. 1), we now report the synthesis of the para-d isomer, rac-(3R,6aS,11aR)-2-methyl-1,3,4,5,6,11a-hexahydro-2H-3,6a-methanobenzofuro[2,3-c]azocin-8-ol (3). Compound 3 was synthesized via construction of the 5-phenylazabicyclo[3.3.1]non-3-ene skeleton (Scheme 1) and subsequent closure of the epoxy bridge (Scheme 2). As determined by an X-ray diffraction study, the epoxy bridge, restricting the phenyl-ring rotation, fixed the dihedral angle between the least-squares planes through the phenyl ring and atoms N(2), C(3), C(11a), and C(6a) of the piperidine ring (Fig. 2) at 43.0°, and the torsion angle C(12)C(6a)C(6b)C(10a) at −95.0°.

Docking of Protein−Protein Complexes on the Basis of Highly Ambiguous Intermolecular Distance Restraints Derived from 1HN/15N Chemical Shift Mapping and Backbone 15N−1H Residual Dipolar Couplings Using Conjoined Rigid Body/Torsion Angle Dynamics

Abstract: A simple and reliable method for docking protein−protein complexes using 1HN/15N chemical shift mapping and backbone 15N−1H residual dipolar couplings is presented and illustrated with three complexes (EIN-HPr, IIAGlc-HPr, and IIAMtl-HPr) of known structure. The 1HN/15N chemical shift mapping data are transformed into a set of highly ambiguous, intermolecular distance restraints (comprising between 400 and 3000 individual distances) with translational and some degree of orientational information content, while the dipolar couplings provide information on relative protein−protein orientation. The optimization protocol employs conjoined rigid body/torsion angle dynamics in simulated annealing calculations. The target function also comprises three nonbonded interactions terms: a van der Waals repulsion term to prevent atomic overlap, a radius of gyration term (Ergyr) to avoid expansion at the protein−protein interface, and a torsion angle database potential of mean force to bias interfacial side chain confo...

Vicinal disulfide turns

Abstract: The formation of a disulfide bond between adjacent cysteine residues is accompanied by the formation of a tight turn of the protein backbone. In nearly 90% of the structures analyzed a type VIII turn was found. The peptide bond between the two cysteines is in a distorted trans conformation, the omega torsion angle ranges from 159 to -133degrees, with an average value of 171degrees. The constrained nature of the vicinal disulfide turn and the pronounced difference observed between the oxidized and reduced states, suggests that vicinal disulfides may be employed as a 'redox-activated' conformational switch.

Conformational effects on optical rotation. 3-substituted 1-butenes.

Abstract: The specific rotations of 2-substituted butanes (X = F, Cl, CN, and HCC) were calculated at the B3LYP/aug-cc-pVDZ level as a function of the C−C−C−C torsion angle. The results for the four compounds are remarkably similar, despite large differences in the electronic transition energies. The temperature dependence of the specific rotations for 2-methylbutyronitrile and for 2-chlorobutane was studied to give experimental information about the effect of the torsion angle on the specific rotation. The results were in good accord with B3LYP/aug-cc-pVDZ calculations. The specific rotations derived from the study of 2-chlorobutane are similar to those previously obtained for 3-chloro-1-butene, indicating that the double bond does not have a large effect on the optical rotations, but it did lead to a large difference between calculated and observed specific rotations.

The Source of Helicity in Perfluorinated N-Alkanes

Abstract: The well-known helical conformations of double stranded DNA and poly(alanine) are stabilized by inter- and intramolecular hydrogen bonds, respectively. Perfluorinated n-alkanes also exhibit stable helical conformations, with ordered chiralities at low temperatures. In the absence of hydrogen bonds, one may ask what forces stabilize perfluorinated n-alkane helices. We combine ab initio and empirical data to study the likely classical source of this helical behavior. Past studies point to bad sterics (van der Waals interactions) between neighboring fluorine atoms as the source of helicity in perfluorinated linear alkanes. In these early studies electrostatics were ignored. We undertook a detailed force field parameter optimization strategy, using experimental and ab initio data, to obtain transferable, uncorrelated estimates of the separate classical energy components. We find that the dominant energy term, the source of helicity, is electrostatics. The coulomb repulsion, from a classical fixed-charge model, reproduces reasonably well the position of the energy minima and the energy barrier between the helical and the all-trans conformations. Polarization effects, changes in atomic charges as a result of conformational changes, are not significant. Dihedral interactions and van der Waals terms adjust the exact position of the minima only slightly. In the absence of electrostatic contributions, van der Waals and dihedral interactions predict the incorrect stable conformations.

Si–O–Si bond angle and torsion angle distribution in vitreous silica and sodium silicate glasses

Abstract: Si–O–Si bond angle distribution (BAD) and torsion angle distribution (TAD) of vitreous silica and sodium silicate glasses have been studied using molecular dynamics simulation, and compared extensively with experimental and computational data. Correlations were investigated between the two angle distributions and the shoulder at 3.7 A in total correlation function. Analysis of the simulated glass structures shows that, because TAD has preference for staggered configurations at low Si–O–Si angles due to steric effects, the shoulder is mainly associated with the width of the BAD. Whereas a smooth shoulder at 3.7 A with a stagger-preferred TAD indicates a broad Si–O–Si BAD for vitreous silica, an emerging hump at 3.7 A reveals the narrowing of the BAD on adding sodium. Finally, various Si–O–Si BADs from the literature are analyzed and a model for the BAD is proposed.

Conformational Analysis of Alanine Dipeptide from Dipolar Couplings in a Water-Based Liquid Crystal

Abstract: The proton NMR spectra of unlabeled alanine dipeptide (Ac-L-Ala-NHMe) at 300 MHz and of alanine dipeptide with a single 13C label at 500 MHz are obtained in the lyotropic liquid-crystalline solvent cesium pentadecafluorooctanoate in water (CsPFO/H2O). Simulations of the spectra yield 9 and 13 dipolar couplings Dij, respectively, many with absolute sign determined. We fit the set of dipolar couplings by systematically varying the flexible dihedral angles φ and ψ while freezing local geometric details from the electronic structure calculations of Suhai and co-workers (Han, W. G.; Jalkanen, K. J.; Elstner, M.; Suhai, S. J. Phys. Chem. B 1998, 102, 2587). The orientation tensor is optimized at each combination of dihedral angles. Remarkably, a single conformer PII (φ ≈ −85°, ψ ≈ +160°) fits both sets of couplings within experimental error. The orientation tensor can be understood in terms of a simple rocking motion that dips the central methyl group into the fluorocarbon core of the CsPFO bicelle while altern...

The Structure of Alanine Based Tripeptides in Water and Dimethyl Sulfoxide Probed by Vibrational Spectroscopy

Abstract: We have measured the band profile of amide I in the infrared, isotropic, and anisotropic Raman spectra of cationic l-alanyl-d-alanyl-l-alanine, l-lysyl-l-alanine-l-alanine, and l-seryl-l-alanine-l-alanine in D2O. Additionally, we recorded spectra of N-acetyl-l-alanyl-l-alanine in D2O and in DMSO-d6. The respective intensity ratios of the two amide I bands depend on excitonic coupling between the amide I modes of the two peptides. These intensity ratios were obtained from a spectral decomposition and then used to determine the dihedral angles between the peptide groups by means of a recently developed algorithm (Schweitzer-Stenner, Biophys. J., 83, 83, 523, 2002). The validity of the obtained structures was checked by measuring the vibrational circular dichroism of the amide I bands. l-Lysyl-l-alanyl-l-alanine, l-seryl-l-alanyl-l-alanine, and acetyl-l-alanyl-l-alanine adopt structures similar to that observed for l-alanyl-l-alanyl-l-alanine. This suggests that the N-terminal residues do not significantly i...

Fine Tuning of Photophysical Properties of meso–meso-Linked ZnII–Diporphyrins by Dihedral Angle Control

Abstract: A series of meso-meso-linked diporphyrins S(n) strapped with a dioxymethylene group of various length were synthesized by intramolecular Ag(I)-promoted coupling of dioxymethylene-bridged diporphyrins B(n), for n=10, 8, 6, 5, 4, 3, 2, and 1. Shortening of the strap length causes a gradual decrease in the dihedral angle between the porphyrins and increasing distortion of porphyrin ring, as suggested by MM2 calculations and (1)H NMR studies. This trend has been also suggested by X-ray crystallographic studies on the corresponding Cu(II) complexes of nonstrapped diporphyrin 2 Cu, and strapped diporphyrins S(8)Cu, S(4)Cu, and S(2)Cu. The absorption spectrum of relatively unconstrained diporphyrins S(10) strapped with a long chain exhibits split Soret bands at 414 and 447 nm and weak Q(0,0)- and prominent Q(1,0)-bands, both of which are similar to those of nonstrapped diporphyrin 2. Shortening of the strap length causes systematic changes in the absorption spectra, in which the intensities of the split Soret bands decrease, the absorption bands at about 400 nm and > 460 nm increase in intensity, and a prominent one-band feature of a Q-band is changed to a distinct two-band feature with concurrent progressive red-shifts of the lowest Q(0,0)-band. The fluorescence spectra also exhibit systematic changes, roughly reflecting the changes of the absorption spectra. The strapped diporphyrins S(n) are all chiral and have been separated into enantiomers over a chiral column. The CD spectra of the optically active S(n) display two Cotton effects at 430-450 and at about 400 nm with the opposite signs. The latter effect can be explained in terms of oblique arrangement of m( perpendicular 1) and m( perpendicular 2) dipole moments, while the former effect cannot be accounted for within a framework of the excition coupling theory. The resonance Raman (RR) spectra taken for excitation at 457.9 nm are variable among S(n), while the RR spectra taken for excitation at 488.0 nm are constant throughout the S(n) series. These photophysical properties can be explained in terms of INDO/S-SCI calculations, which have revealed charge transfer (CT) transitions accidentally located close in energy to the excitonic Soret transitions. This feature arises from a close proximity of the two porphyrins in meso-meso-linked diporphyrins. In addition to the gradual red-shift of the exciton split Soret band, the calculations predict that the high-energy absorption band at about 400 nm, the lower energy Cotton effect, and the RR spectra taken for excitation at 457.9 nm are due to the CT states which are intensified upon a decrease in the dihedral angle.

Sterically Encumbered Diphosphaalkenes and a Bis(diphosphene) as Potential Multiredox-Active Molecular Switches: EPR and DFT Investigations

Abstract: The reduction products of two diphosphaalkenes (1 and 2) and a bis(diphosphene) (3) containing sterically encumbered ligands and corresponding to the general formulas Ar−XY−Ar‘−YX−Ar, have been investigated by EPR spectroscopy. Due to steric constraints in these molecules, at least one of the dihedral angles between the CXYC plane and either the Ar plane or the Ar‘ plane is largely nonzero and, hence, discourages conformations that are optimal for maximal conjugation of PX (or PY) and aromatic π systems. Comparison of the experimental hyperfine couplings with those calculated by DFT on model systems containing no cumbersome substituents bound to the aromatic rings shows that addition of an electron to the nonplanar neutral systems causes the XY−Ar‘−YX moiety to become planar. In contrast to 1 and 2, 3 can be reduced to relatively stable dianion. Surprisingly the two-electron reduction product of 3 is paramagnetic. Interpretation of its EPR spectra, in the light of DFT calculations on model dianions, shows...

Tiling space and slabs with acute tetrahedra

Abstract: We show it is possible to tile three-dimensional space using only tetrahedra with acute dihedral angles. We present several constructions to achieve this, including one in which all dihedral angles are less than $77.08^\circ$, and another which tiles a slab in space.

Correlated motions of successive amide N-H bonds in proteins

Abstract: New nuclear magnetic resonance (NMR) methods are described for the measurement of cross-correlation rates of zero- and double-quantum coherences involving two nitrogen nuclei belonging to successive amino acids in proteins and peptides. Rates due to the concerted fluctuations of two NHN dipole-dipole interactions and to the correlated modulations of two nitrogen chemical shift anisotropies have been obtained in a sample of doubly labeled Ubiquitin. Ambiguities in the determination of dihedral angles can be lifted by comparison of different rates. By defining a heuristic order parameter, experimental rates can be compared with those expected for a rigid molecule. The cross-correlation order parameter that can be derived from a model-free approach can be separated into structural and dynamic contributions.

Low-spin ferriheme models of the cytochromes: correlation of molecular structure with EPR spectral type.

Abstract: The preparation and characterization of the following bis-imidazole and bis-pyridine complexes of octamethyltetraphenylporphyrinatoiron(III), Fe(III)OMTPP, octaethyltetraphenylporphyrinatoiron(III), Fe(III)OETPP, and tetra-beta,beta'-tetramethylenetetraphenylporphyrinatoiron(III), Fe(III)TC(6)TPP, are reported: paral-[FeOMTPP(1-MeIm)(2)]Cl, perp-[FeOMTPP(1-MeIm)(2)]Cl, [FeOETPP(1-MeIm)(2)]Cl, [FeTC(6)TPP(1-MeIm)(2)]Cl, [FeOMTPP(4-Me(2)NPy)(2)]Cl, and [FeOMTPP(2-MeHIm)(2)]Cl. Crystal structure analysis shows that paral-[FeOMTPP(1-MeIm)(2)]Cl has its axial ligands in close to parallel orientation (the actual dihedral angle between the planes of the imidazole ligands is 19.5 degrees ), while perp-[FeOMTPP(1-MeIm)(2)]Cl has the axial imidazole ligand planes oriented at 90 degrees to each other and 29 degrees away from the closest N(P)-Fe-N(P) axis. [FeOETPP(1-MeIm)(2)]Cl has its axial ligands close to perpendicular orientation (the actual dihedral angle between the planes of the imidazole ligands is 73.1 degrees ). In all three cases the porphyrin core adopts relatively purely saddled geometry. The [FeTC(6)TPP(1-MeIm)(2)]Cl complex is the most planar and has the highest contribution of a ruffled component in the overall saddled structure compared to all other complexes in this study. The estimated numerical contribution of saddled and ruffled components is 0.68:0.32, respectively. Axial ligand planes are perpendicular to each other and 15.3 degrees away from the closest N(P)-Fe-N(P) axis. The Fe-N(P) bond is the longest in the series of octaalkyltetraphenylporphyrinatoiron(III) complexes due to [FeTC(6)TPP(1-MeIm)(2)]Cl having the least distorted porphyrin core. In addition to these three complexes, two crystalline forms each of [FeOMTPP(4-Me(2)NPy)(2)]Cl and [FeOMTPP(2-MeHIm)(2)]Cl were obtained. In all four of these cases the axial planes are in nearly perpendicular planes in spite of quite different geometries of the porphyrin cores (from purely saddled to saddled with 30% ruffling). The EPR spectral type correlates with the geometry of the OMTPP, OETPP and TC(6)TPP complexes. For the paral-[FeOMTPP(1-MeIm)(2)]Cl, a rhombic signal with g(1) = 1.54, g(2) = 2.51, and g(3) = 2.71 is consistent with nearly parallel axial ligand orientation. For all other complexes of this study, "large g(max)" signals are observed (g(max) = 3.61 - 3.27), as are observed for nearly perpendicular ligand plane arrangement. On the basis of this and previous work, the change from "large g(max)" to normal rhombic EPR signal occurs between axial ligand plane dihedral angles of 70 degrees and 30 degrees.

Theoretical and spectroscopic study of a series of styryl-substituted terthiophenes

Abstract: Molecular structures of a series of 3'-[1E-2-(4-R-phenyl)ethenyl]-2,2':5',2"-terthiophenes have been modeled using ab initio calculations. The potential energy surfaces of three important dihedral angles were calculated using the HF/3-21G(d) method. Each dihedral angle is represented by a distinct potential energy surface, while the identity of the R group has only a modest influence. DFT methods (B3LYP/6-31G(d)) were used to calculate the geometry and vibrational spectra of each molecule. Analysis of the theoretical vibrational data reveals numerous conserved modes that are localized on the terthiophene or phenyl groups. There is good agreement between the observed and calculated vibrational spectra of the molecules. Conformational changes have only a minor effect on the spectra. The calculated molecular orbitals, which are supported by electronic absorption measurements, suggest that the first excited state should have charge-transfer features for the molecules with strongly electron withdrawing or donating substituents.

New theoretical studies on the dihedral angle and energy barriers of biphenyl

Abstract: Using Hartree–Fock (HF), Moller–Plesset (MP2) and the B3LYP, B3PW91 and MPW1PW91 density functional (DF) methods, each combined with the 6-31G(d), 6-311G(d), 6-311+G(d), 6-311++G(d,p), cc-pVDZ amd cc-pVTZ basis sets, the geometry of biphenyl was optimized and the energy barriers at 0°, Δ E 0 , and 90°, Δ E 90 , were obtained. For the best basis sets (6-311++G(d,p) and cc-pVTZ), the DF methods lead to dihedral angles φ from 39 to 41° (44.4±1.2°) experimental), Δ E 0 's from 1.9 to 2.3 kcal/mol (the experimental estimate is 1.4±0.5 kcal/mol), and Δ E 90 's from 1.9 to 2.3 kcal/mol (the experimental estimate is 1.6±0.5 kcal/mol). With the MP2 method, however, the results depend drastically on the basis set. With cc-pVTZ, all three quantities are close to the DF values, but with the 6-311++G(d,p) basis set, φ is 47.7°, Δ E 0 4.4 kcal/mol and Δ E 90 1.6 kcal/mol. The MP2 method appears to show a trend towards a more coplanar conformation, expected for methods that include electron correlation, only with highly polarized basis sets.

The internal coordinate path Hamiltonian; application to methanol and malonaldehyde

Abstract: The internal coordinate path Hamiltonian is introduced for the study of the vibrations of molecules which have one large amplitude motion. The Hamiltonian is represented in terms of a one path coordinate and 3N—7 normal coordinates. The variational method is used to solve the Schrodinger equation. The molecules studied are methanol and malonaldehyde. For methanol the internal coordinate is a dihedral angle, for malonaldehyde it is the difference in the distances between the migrating hydrogen and the neighbouring oxygen atoms. For methanol there is little coupling between the path and the normal coordinates and so no complications were encountered in the calculations which used harmonic surfaces generated by density functional and M⊘ller—Plesset theory. Fundamental frequencies were predicted. Malonaldehyde is a different story. There is substantial coupling between the path coordinate and several of the normal coordinates. This introduces many complications: an anharmonic surface is essential and large va...

Helical twisting power and scaled chiral indices

Abstract: Chirality of optically active liquid crystal molecules has become an important research topic and the subject of a number of theoretical and experimental studies. We present here the results of the application of a newly developed scaling method of a chiral index to a range of chiral molecules. Good agreement is found between the scaled chiral index and the helical twisting power for relatively rigid molecules. Two flexible TADDOL (α,α,α′,α′-tetraaryl-1,3-dioxolan-4,5dimethanol) molecules are studied to determine which conformations may give rise to their high experimental helical twisting powers. A variety of links between the moment of inertia tensor, the dihedral angles, the scaled chiral indices, the minimum energy of the optimized geometry and the experimental helical twisting power are discussed. The scaled chiral and steric indices and dihedral angles are promising as predictors of experimental helical twisting power, in particular for relatively rigid molecules, in cases where all the relevant interactions are determined by the molecular structure.

Structural and dynamical changes of the bindin B18 peptide upon binding to lipid membranes. A solid-state NMR study.

Abstract: Structural and dynamical features of the B18 peptide from the sea urchin sperm bindin protein were determined in the crystalline state and in zwitterionic lipid bilayers at a peptide:lipid molar ratio of 1:12 using solid-state NMR spectroscopy. The study was focused on three 13C and 15N uniformly labeled leucine residues, which were introduced into three different B18 peptides at positions evenly distributed along the B18 primary structure. Isotropic 13C and 15N chemical shift measurements showed that while B18 possesses a nonhelical and non-sheet-like structure in the crystalline state, the peptide adopts an oligomeric β-sheet structure in the membrane in the presence of Zn2+ ions at high peptide:lipid ratio. Torsion angle measurements for the three leucine sites supported these results, with φ torsion angles between −80° and −90° in the crystalline state and between −110° and −120° in the membrane-bound form. These φ torsion angles determined for membrane-bound B18 are consistent with a parallel β-sheet...

Base pair analogs in the gas phase

Abstract: A rotationally resolved electronic spectrum of the gas-phase dimer 2-aminopyridine·2-pyridone, an analog of the adenine·thymine base pair, has been observed and assigned, leading to precise measurements of its moments of inertia and preliminary determinations of its structure. A Watson–Crick configuration results, with N···H—N and N—H···O hydrogen bond lengths of 2.898 and 2.810 A, respectively. The two bases are found not to be coplanar; a dihedral angle of 6.1° between the base planes is also estimated from the measured moments of inertia. Possible chemical and biological implications of these results are discussed.

Twisted π-system electro-optic chromophores. A CIS vs. MRD-CI theoretical investigation

Abstract: Twisted, merocyanine-type molecules are investigated theoretically as chromophores, whose optical and electro-optic responses can be controlled via steric repulsion-mediated tuning of the central dihedral angle. Employing multi-reference determinant computational methods results in significant modifications to the quantitative aspects of the response properties, compared to values computed using a single determinant ground state, and leads to computed hyperpolarizabilities even larger than previously estimated. Using either computational approach demonstrates that fine control of the sharp variations in response properties can be achieved by using substituent-induced steric repulsions to modify the internal dihedral twist angles.