Showing papers on "Dihedral angle published in 2001"
TL;DR: A series of optically active diphosphine ligands, (4,4′-bi-1,3-benzodioxole)-5,5′-diylbis(diarylphosphine)s (6), which are called SEGPHOS, has been designed and synthesized with dihedral angles in the Ru complexes being less than that in the corresponding BINAP-Ru complex as mentioned in this paper.
Abstract: A series of novel optically active diphosphine ligands, (4,4′-bi-1,3-benzodioxole)-5,5′-diylbis(diarylphosphine)s (6), which are called SEGPHOS, has been designed and synthesized with dihedral angles in the Ru complexes being less than that in the corresponding BINAP-Ru complex. The stereorecognition abilities of SEGPHOS-Ru complex catalysts in the asymmetric catalytic hydrogenation of a wide variety of carbonyl compounds are superior to those observed with BINAP-Ru complex catalysts.
356 citations
TL;DR: The results explain the Am III frequency dependence on conformation as well as the resonance Raman enhancement mechanism for the (C)C(alpha)H bending UV Raman band.
Abstract: UV resonance Raman studies of peptide and protein secondary structure demonstrate an extraordinary sensitivity of the amide III (Am III) vibration and the CαH bending vibration to the amide backbone conformation. We demonstrate that this sensitivity results from a Ramachandran dihedral ψ angle dependent coupling of the amide N−H motion to (C)CαH motion, which results in a ψ dependent mixing of the Am III and the (C)CαH bending motions. The vibrations are intimately mixed at ψ ∼ 120°, which is associated with both the β-sheet conformation and random coil conformations. In contrast, these motions are essentially unmixed for the α-helix conformation where ψ ∼ −60°. Theoretical calculations demonstrate a sinusoidal dependence of this mixing on the ψ angle and a linear dependence on the distance separating the N−H and (C)CαH hydrogens. Our results explain the Am III frequency dependence on conformation as well as the resonance Raman enhancement mechanism for the (C)CαH bending UV Raman band. These results may ...
185 citations
TL;DR: The structural and thermodynamic properties of a 6-residue beta-peptide that was designed to form a hairpin conformation have been studied by NMR spectroscopy and MD simulation in methanol solution and there is a significant conformational overlap between the unfolded state of the peptide at each of the temperatures.
Abstract: The structural and thermodn. properties of a 6-residue β-peptide I that was designed to form a hairpin conformation have been studied by NMR spectroscopy and mol. dynamics simulation in methanol soln. The predicted hairpin would be characterized by a 10-membered hydrogen-bonded turn involving residues 3 and 4, and two extended antiparallel strands. The interproton distances and backbone torsional dihedral angles derived from the NMR expts. at room temp. are in general terms compatible with the hairpin conformation. Two trajectories of system configurations from 100-ns mol.-dynamics simulations of the peptide in soln. at 298 and 340 K have been analyzed. In both simulations, reversible folding to the hairpin conformation is obsd. Interestingly, there is a significant conformational overlap between the unfolded state of the peptide at each of the temps. As already obsd. in previous studies of peptide folding, the unfolded state is composed of a (relatively) small no. of predominant conformers and in this case lacks any type of secondary-structure element. The trajectories provide an excellent ground for the interpretation of the NMR-derived data in terms of ensemble avs. and distributions as opposed to single-conformation interpretations. From this perspective, a relative population of the hairpin conformation of 20% to 30% would suffice to explain the NMR-derived data. Surprisingly, however, the ensemble of structures from the simulation at 340 K reproduces more accurately the NMR-derived data than the ensemble from the simulation at 298 K, and this point needs further investigation.
174 citations
TL;DR: The square grid structure of MOF-2, constructed from Zn(II) and 1,4-benzenedicarboxylate (BDC) links, persists for 2-amino-1,4,6-tetramethyl-ABDC links but not for the sterically demanding 2,3,5,6,tetramerethyl-1-4,7,6tetamethyl-TBDC links as discussed by the authors.
160 citations
TL;DR: A remarkable correlation is found suggesting that the concept of secondary chemical shifts, well established in the liquid state, can be of similar importance in the context of multiple-labelled polypeptides studied under MAS conditions.
Abstract: Resonance assignments recently obtained on immobilized polypeptides and a membrane protein aggregate under Magic Angle Spinning are compared to random coil values in the liquid state. The resulting chemical shift differences (secondary chemical shifts) are evaluated in light of the backbone torsion angle ψ previously reported using X-ray crystallography. In all cases, a remarkable correlation is found suggesting that the concept of secondary chemical shifts, well established in the liquid state, can be of similar importance in the context of multiple-labelled polypeptides studied under MAS conditions.
150 citations
TL;DR: In this paper, the amide I band of an alanine-based 21-residue α-helical peptide in aqueous solution was investigated using nonlinear two-dimensional (2D) vibrational spectroscopy.
Abstract: Nonlinear two-dimensional (2D) vibrational spectroscopy has been used to investigate the amide I band of an alanine-based 21-residue α-helical peptide in aqueous solution. Whereas the linear absorption spectrum consists of a single, broad amide I band, the 2D vibrational spectrum clearly reveals that this band is composed of two amide I transitions, which are assigned to the A and E1 modes. The A–E1 frequency splitting is found to be approximately 10 cm−1. We find that the amide I band is inhomogeneously broadened due to conformational disorder of the helix. The 2D line shapes can be well described using distributions of the dihedral angles (φ,ψ) around their average values with a width of 20°, confirming previous molecular-dynamics studies. Time-resolved 2D measurements show that the conformation fluctuates on a time scale of picoseconds.
143 citations
TL;DR: This study provides compelling evidence that tripeptides adopt stable conformations in aqueous solution and that they are suitable model systems to investigate the initiation of secondary structure formation.
Abstract: We have measured the polarized visible Raman and FTIR spectra of trialanine and triglycine in D(2)O at acid, neutral, and alkaline pD. From the Raman spectra we obtained the isotropic and the anisotropic scattering. A self-consistent spectral analysis of the region between 1550 and 1800 cm(-1) was carried out to obtain the intensities, frequencies, and halfwidths of the respective amide I bands. A model was developed by means of which the intensity ratios of the amide I bands in all spectra and the respective frequency differences were utilized to determine the orientational angle theta between the peptide groups and the strength of excitonic coupling between the corresponding amide I modes. By exploiting results from a recent ab initio study on triglycine (Torii, H; Tasumi, M. J. Raman Spectrosc. 1998, 29, 81), we used these parameters to determine the dihedral angles phi and psi between the peptide groups. Our results show that trialanine adopts a 3(1)-helical structure in D(2)O for all of its three protonation states. The structure is insensitive to the carboxylate protonation and changes only slightly with N-terminal protonation. Triglycine is structurally more heterogeneous in the zwitterionic and the cationic state. Our spectral analysis suggests that 3(1)-helices coexist with right-handed alpha-helical and/or with beta-turn conformations. The N-terminal protonation stabilizes the 3(1)-structure. Our study provides compelling evidence that tripeptides adopt stable conformations in aqueous solution and that they are suitable model systems to investigate the initiation of secondary structure formation.
132 citations
TL;DR: The MO calculations indicate that the quasiorthogonality between the magnetic orbital of metal ions and the p atomic orbitals of the bridging azide is possible in the observed structures and leads to the ferromagnetism.
Abstract: Two new one-dimensional single azide-bridged metal(II) compounds [[M(5-methylpyrazole)4(N3)]n](ClO4)n(H2O)n [M = Co (1a), Ni (2a)] were prepared by treating an M(II) ion with stoichiometric amount of sodium azide in the presence of four equivalents of the 3(5)-methylpyrazole ligand. The isostructural compounds 1a and 2a crystallize in the monoclinic space group P2(1)/n. The azide bridging ligands have a unique end-to-end coordination mode that brings two neighboring metal centers into a cis-position with respect to the azide unit to form single end-to-end azide-bridged cobalt(II) and nickel(II) chains. The two neighboring metal atoms at inversion centers adopt octahedral environments with four equatorial 3(5)-methylpyrazole ligands and two axial azide bridges. Two adjacent equatorial least-squares planes form dihedral angles of 60.5 degrees and 60.6 degrees for Co and Ni, respectively. In addition, the metal-azide-metal units form large M-N3-M torsion angles, which are magnetically important geometrical parameters, of 71.6 degrees for M=Co and 75.7 degrees for M=Ni. It should also be noted that the M-N-N angles associated with end-to-end azide group, another magnetically important structural parameter, fall into the experimentally observed range of 120-140 degrees as 128.3(3) and 147.8(3) degrees for cobalt species and 128.4(2) and 146.1(3) degrees for nickel species; these values deviate from the theoretical value of around 164 degrees at which the incidental orthogonality is achieved under the torsion angle of 0 degrees. The compounds 1a and 2a have unique magnetic properties of ferromagnetism, zero-field splitting, and spin canting. The MO calculations indicate that the quasiorthogonality between the magnetic orbitals of metal ions and the p atomic orbitals of the bridging azide is possible in the observed structures and leads to the ferromagnetism. The spin canting related to the perturbation of ferromagnetism arises from the magnetic anisotropy and antisymmetric interactions judged by the structural parameters of the zero-field splitting and the tilted MN4 planes in a chain. The enhancement of magnetic interactions was accomplished by dehydrating the chain compounds to afford two soft magnets with critical temperature T(C) and coercive field of 2 K and 35 G for 1b and 2.3 K and 20 G for 2b, respectively.
122 citations
TL;DR: In this paper, a linear combination of ideal basic conformations is used to characterize six-membered ring conformations, which is based on endocyclic dihedral angles.
97 citations
TL;DR: In this article, the absorption and vibrational circular dichroism (VCD) spectra of six 1,1'-binaphthyl derivatives were measured and analyzed on the basis of ab initio modeling.
Abstract: Absorption and vibrational circular dichroism (VCD) spectra of six 1,1‘-binaphthyl derivatives were measured and analyzed on the basis of ab initio modeling. The spectra of both enantiomers were recorded with a high signal-to-noise ratio. The BPW91/6-31G** density functional theory level and the gauge invariant atomic orbitals were used for the simulations of VCD intensities. The binaphthyl moiety behaves as a chiral chromophore with a strong VCD signal because the 1,1‘-substitution hinders its rotation. Most of the VCD bands were assigned, and the contributions of the binaphthyl skeleton and the functional groups could be clearly distinguished. Distinct VCD characteristics were found for the compounds exhibiting C2 and C1 symmetry. A very good agreement between the calculated and experimental spectra was observed. Apart from indication of enantiomeric purity, the spectra contain readable information about molecular conformation. The dihedral angle between the naphthyls planes, equal to about 55° when nap...
83 citations
TL;DR: In this article, 1-[N-(4-chlorophenyl)]aminomethylidene-2(1H)naphthalenone (C17H12NOCl) (1) was synthesized and the crystal structure was determined.
Abstract: 1-[N-(4-chlorophenyl)]aminomethylidene-2(1H)naphthalenone (C17H12NOCl) (1) was synthesized and the crystal structure was determined. Compound 1 crystallizes in the monoclinic space group P21/n with a = 4.761(3) A, b = 20.347(1) A, c = 13.773(2) A, β = 92.89(3)°, V = 1332.4(3) A3, Z = 4, D
c = 1.404 g cm−3, μ(Mo Kα) = 0.28 mm−1, and R = 0.036 for 2680 reflections [I > 2σ(I)]. Molecule 1 is not planar, and the dihedral angle between the naphthaldeyde plane A [C1–C11, 01] and the 4-chloroaniline plane B [C12–C17, C11, N1] is 20.1(3)°. An intramolecular hydrogen bond occurs between the hydroxyl oxygen and imine nitrogen atoms [2.528(3) A]. IR, 1H NMR, and UV measurements and AM1 semiempirical quantum mechanical calculations support the keto form found in the X-ray structure.
TL;DR: Dynamic aspects of alkane hydroxylation mediated by Compound I of cytochrome P450 are discussed from classical trajectory calculations at the B3LYP level of density functional theory and an important issue about which normal mode of vibration is activated during the hydroxymatic reaction is investigated in detail.
Abstract: Dynamic aspects of alkane hydroxylation mediated by Compound I of cytochrome P450 are discussed from classical trajectory calculations at the B3LYP level of density functional theory. The nuclei of the reacting system are propagated from a transition state to a reactant or product direction according to classical dynamics on a Born-Oppenheimer potential energy surface. Geometric and energetic changes in both low-spin doublet and high-spin quartet states are followed along the ethane to ethanol reaction pathway, which is partitioned into two chemical steps: the first is the H-atom abstraction from ethane by the iron-oxo species of Compound I and the second is the rebound step in which the resultant iron-hydroxo complex and the ethyl radical intermediate react to form the ethanol complex. Molecular vibrations of the C-H bond being dissociated and the O-H bond being formed are significantly activated before and after the transition state, respectively, in the H-atom abstraction. The principal reaction coordinate that can represent the first chemical step is the C-H distance or the O-H distance while other geometric parameters remain almost unchanged. The rebound process begins with the iron-hydroxo complex and the ethyl radical intermediate and ends with the formation of the ethanol complex, the essential process in this reaction being the formation of the C-O bond. The H-O-Fe-C dihedral angle corresponds to the principal reaction coordinate for the rebound step. When sufficient kinetic energy is supplied to this rotational mode, the rebound process should efficiently take place. Trajectory calculations suggest that about 200 fs is required for the rebound process under specific initial conditions, in which a small amount of kinetic energy (0.1 kcal/mol) is supplied to the transition state exactly along the reaction coordinate. An important issue about which normal mode of vibration is activated during the hydroxylation reaction is investigated in detail from trajectory calculations. A large part of the kinetic energy is distributed to the C-H and O-H stretching modes before and after the transition state for the H-atom abstraction, respectively, and a small part of the kinetic energy is distributed to the Fe-O and Fe-S stretching modes and some characteristic modes of the porphyrin ring. The porphyrin marker modes of nu(3) and nu(4) that explicitly involve Fe-N stretching motion are effectively enhanced in the hydroxylation reaction. These vibrational modes of the porphyrin ring can play an important role in the energy transfer during the enzymatic process.
TL;DR: In this article, two conjugating helical polymers, poly{(R)-3,7-dimethyloctyl-(S)-3-methylpentylsilylene} (PS-1) and its diastereomeric poly {(S)- 3,7,dimethyl-octyl--(S),3- methylpentyl-silylen} (Ps-2), were prepared.
Abstract: Two new conjugating helical polymers comprising a rodlike silicon backbone and enantiopure chiral pendants, poly{(R)-3,7-dimethyloctyl-(S)-3-methylpentylsilylene} (PS-1) and its diastereomeric poly{(S)-3,7-dimethyloctyl-(S)-3-methylpentylsilylene} (PS-2), were prepared. Molecular mechanics calculations of PS-1 and PS-2 model oligomers indicated a double well potential energy curve corresponding to almost enantiomeric helices with dihedral angles of 150−160° (P-motif, global minimum) and 200−210° (M-motif), regardless of their tacticity. Experimentally, it was found that PS-1 in dilute isooctane revealed switchable ambidextrous helicity on application of a thermal energy bias. Although PS-1 featured three distinct switching regions, viz. “region 1, between −80 and −10 °C”, “region 2, between −10 and +10 °C”, and “region 3, between +10 °C and +80 °C”, the switching properties were interpreted as the result of superposed P- and M-helicities, undergoing dynamic pseudo-racemization or oscillation. Oscillating ...
TL;DR: A series of tin-lithium exchange experiments indicate that the configurational stability of a carbamate-stabilized organolithium species may be enhanced by restrictive geometry.
Abstract: A series of selected bicyclic carbamates in which the range of accessible angles and distances between the carbonyl group and the proton removed in an alpha-lithiation reaction are structurally defined have been investigated. Oxazolidinones 7-10 undergo stereoselective lithiation-substitution reactions to provide cis-18-27 and cis-31-35 as the major diastereomers. Two series of competition experiments show that the conformationally restricted carbamates 7, 10, 11, and 15 undergo lithiation via complexes more efficiently than Boc amines 4-6. These results along with semiempirical calculations suggest that a small dihedral angle and a calculated distance of 2.78 A between the carbamate carbonyl oxygen and the proton to be removed are favorable for a carbamate-directed lithiation. A series of tin-lithium exchange experiments on cis- and trans-18 and (S)-39 indicate that the configurational stability of a carbamate-stabilized organolithium species may be enhanced by restrictive geometry.
TL;DR: This study demonstrates that dipolar couplings may be used to characterize both the conformation of static residues and side-chain motion with high precision.
Abstract: Experiments are presented for the measurement of one-bond carbon−proton dipolar coupling values at CH and CH2 positions in 13C-labeled, ∼50% fractionally deuterated proteins 13Cβ−1Hβ dipolar couplings have been measured for 38 of 49 possible residues in the 63-amino-acid B1 domain of peptostreptococcal protein L in two aligning media and interpreted in the context of side-chain χ1 torsion angle dynamics The β protons for 18 of the 25 β-methylene-containing amino acids for which dipolar data are available can be unambiguously stereoassigned, and for those residues which are best fit to a single rotamer model the χ1 angles obtained deviate from crystal structure values by only 52° (rmsd) The results for 11 other residues are significantly better fit by a model that assumes jumps between the three canonical (χ1 ≈ −60°, 60°, 180°) rotamers Relative populations of the rotamers are determined to within ±6% uncertainty on average and correlate with dihedral angles observed for the three molecules in the cry
TL;DR: In this article, a solid state NMR technique for the determination of peptide backbone conformations at specific sites in unoriented samples under magic angle spinning (MAS) is described and demonstrated on a doubly labeled polycrystalline sample of the tripeptide AlaGlyGly and a sextuply labeled lyophilized sample of 17-residue peptide MB( i +4)EK.
TL;DR: In this paper, the authors studied the ground, ionic, and excited states of a series of oligomers of thiophene, and showed that the most relevant highest occupied and lowest unoccupied molecular orbitals develop gradually from monomer molecular orbits into occupied and unoccupied broad bands in the large length limit.
Abstract: We present density-functional and time-dependent density-functional studies of the ground, ionic, and excited states of a series of oligomers of thiophene. We show that, for the physical properties, the most relevant highest occupied and lowest unoccupied molecular orbitals develop gradually from monomer molecular orbitals into occupied and unoccupied broad bands in the large length limit. We show that band gap and ionization potentials decrease with size, as found experimentally and from empirical calculations. This gives credence to a simple tight-binding model Hamiltonian approach to these systems. We demonstrate that the length dependence of the experimental excitation spectra for both singlet and triplet excitations can be very well explained with an extended Hubbard-like Hamiltonian, with a monomer on-site Coulomb and exchange interaction and a nearest-neighbor Coulomb interaction. We also study the ground and excited-state electronic structures as functions of the torsion angle between the units in a dimer, and find almost equal stabilities for the transoid and cisoid isomers, with a transition energy barrier for isomerization of only 4.3 kcal/mol. Fluctuations in the torsion angle turn out to be very low in energy, and therefore of great importance in describing even the room-temperature properties. At a torsion angle of 90° the hopping integral is switched off for the highest occupied molecular orbital levels because of symmetry, allowing a first-principles estimate of the on-site interaction minus the next-neighbor Coulomb interaction as it enters in a Hubbard-like model Hamiltonian.
TL;DR: Both the sequences and in vivo effects of all contryphans isolated suggest that there are two major branches of the contryphan family, and Ultraviolet resonance Raman spectroscopy demonstrates a difference in the D-tryptophan dihedral angle for the two contry orphan-Tx equilibrium conformers.
TL;DR: The monoanion of 2,6-bis(phenylamino)pyridine (HBPAP(-)) has been found to support quadruply bonded Cr(2)(4+) and Mo(2(4+) units in Cr (2)(HBP AP)(4) (1) and Mo (2) (2), and the corresponding dianion BPAP( 2)(-) was able to stabilize the trinuclear complexes.
Abstract: The monoanion of 2,6-bis(phenylamino)pyridine (HBPAP(-)) has been found to support quadruply bonded Cr(2)(4+) and Mo(2)(4+) units in Cr(2)(HBPAP)(4) (1) and Mo(2)(HBPAP)(4) (2). The corresponding dianion BPAP(2)(-) was able to stabilize the trinuclear complexes, (TBA)(2)Cr(3)(BPAP)(4) (3) and (TBA)(2)Ni(3)(BPAP)(4) (4), where TBA is the tetrabutylammonium cation. The dinuclear complexes have the typical paddlewheel configuration with Cr-Cr distances of about 1.87 A and a Mo-Mo distance of 2.0813(5) A and exhibit a high-field displacement of the corresponding N-H signals caused by the magnetic anisotropy of the quadruple bonds. For the trinuclear complexes, 3 has a linear chain of three chromium atoms arranged in an unsymmetrical fashion with two chromium atoms paired to give a quadruply bonded unit (Cr-Cr distance: 1.904(3) A) and an isolated, square planar Cr(II) unit at 2.589(3) A from the dimetal unit. On the other hand, the three nickel atoms in 4 are evenly spaced, having Ni.Ni distances of 2.3682(8) A. The trinuclear compounds show a twisted conformation with an overall torsion angle of about 30 degrees.
TL;DR: In this paper, the authors investigated the influence of intermolecular interactions on the optical and structural properties of oligophenyls in solid films of polycrystalline nature, and found a red shift upon increasing pressure in the computed optical absorption spectra which is due to conformational changes of the 2P molecule.
TL;DR: In this article, it was shown that the protein environment of GFP allows the chromophore some rotational freedom, especially by a hula-twist and in the ϕ dihedral angle.
TL;DR: The dihedral angle between both phenyl rings determined by photoelectron spectroscopy in a series of seven alkylbiphenyl compounds is described by the local spectral moments of the bond matrix, proving that 2D (topological) descriptors can account for 3D structural parameters.
Abstract: The dihedral angle between both phenyl rings determined by photoelectron spectroscopy in a series of seven alkylbiphenyl is described by the local spectral moments of the bond matrix. This series is extended to 78 alkylbiphenyl compounds by estimating the dihedral angle from molecular mechanics force field calculations. The linear correlation obtained between this angle and the local spectral moments shown a correlation coefficient of 0.9838. This result proves that 2D (topological) descriptors can account for 3D structural parameters. A new substituent constant is calculated as the contribution of groups to the studied rotational angle by using the information encoded into the local spectral moments. This substituent constant is not linearly related to the Taft's steric constants E(S) as they have a correlation coefficient of only 0.75. These steric constants are able to account only for 71% of the variance in the studied 3D parameter. The implications for QSPR/QSAR studies of the demonstration that 2D (topological) descriptors can describe 3D structural parameters are also analyzed.
TL;DR: The NMR solution structure of oxidized plastocyanin from the cyanobacterium Synechocystis PCC6803 is overall quite satisfactory and represents a breakthrough, in that it includes paramagnetic copper proteins among the metalloproteins for which solution structures can be afforded.
Abstract: The NMR solution structure of oxidized plastocyanin from the cyanobacterium Synechocystis PCC6803 is here reported. The protein contains paramagnetic copper(II), whose electronic relaxation times are quite unfavorable for NMR solution studies. The structure has been solved on the basis of 1041 meaningful NOESY cross-peaks, 18 1D NOEs, 26 T(1) values, 96 dihedral angle constraints, and 18 H-bonds. The detection of broad hyperfine-shifted signals and their full assignment allowed the identification of the copper(II) ligands and the determination of the Cu-S-C-H dihedral angle for the coordinated cysteine. The global root-mean-square deviation from the mean structure for the solution structure family is 0.72 +/- 0.14 and 1.16 +/- 0.17 A for backbone and heavy atoms, respectively. The structure is overall quite satisfactory and represents a breakthrough, in that it includes paramagnetic copper proteins among the metalloproteins for which solution structures can be afforded. The comparison with the available X-ray structure of a triple mutant is also performed.
TL;DR: In this article, the electronic structure of the betaine dye molecule, pyridinium-N-phenoxide [4-(1-pyrinio)phenolate] including the effects of geometry and polar solvents, has been studied at an ab initio level using the reference interaction site model self-consistent field (RISM-SCF) method.
Abstract: The electronic structure of the betaine dye molecule, pyridinium- N-phenoxide [4-(1-pyridinio)phenolate] including the effects of geometry and polar solvents, has been studied at an ab initio level using the reference interaction site model self-consistent-field (RISM-SCF) method. Acetonitrile (CH3CN) and water (H2O) were selected as polar solvents. We obtain both the optimized solute geometry in solution and the total free energy profile with respect to variation in the torsion angle between the pyridinium and phenoxide rings and analyze the various electronic and solvation contributions. The betaine molecule in the gas phase has a twisted geometry, which is slightly more twisted in solution. In acetonitrile, the calculated structure shows good agreement with earlier semiempirical results for the minimum free energy structure. It is shown that the solute dipole moment is strongly enhanced in polar solution, also in accord with earlier semiempirical calculations. However, in solution, there is relatively ...
TL;DR: In this article, the authors used density functional theory (DFT) methods to calculate the proton hyperfine coupling constants for [VO(H2O)5]2+ for equatorial water molecules.
Abstract: Density functional theory (DFT) methods, as implemented in the Amsterdam Density Functional Theory (ADF) program, were used to calculate the proton hyperfine coupling constants for [VO(H2O)5]2+. Qualitative agreement between the calculated and experimental proton hyperfine coupling constants for the axial water molecule in [VO(H2O)5]2+ was observed. For the equatorial water molecules, the proton hyperfine coupling constants depend on the orientation of the water molecule relative to the equatorial plane. DFT calculations revealed that the isotropic component of the proton hyperfine coupling constant for an equatorial water molecule has a trigonometric dependence on β, where β is the OVOH dihedral angle. The relative sizes of the isotropic hyperfine coupling constants for two protons on one water molecule can be used to determine the orientation of the water molecule with respect to the equatorial plane. The computational results were compared with experimental single-crystal and powder ENDOR data from the...
TL;DR: In this paper, the molecular structures of peracylated β-cyclodextrins (CDs)heptakis(2,3,6-tri-O-acetyl)-β-CD (TA), heptakis (2, 3, 6-tri -O-propanoyl)-β -CD (TP), and heptonakis( 2, 3.6-tric-butanoyl-β-cd (TB) have been determined by single crystal X-ray structure analysis.
Abstract: The molecular structures of peracylated β-cyclodextrins (CDs)heptakis(2,3,6-tri-O-acetyl)-β-CD (TA), heptakis(2,3,6-tri-O-propanoyl)-β-CD (TP), and heptakis(2,3,6-tri-O-butanoyl)-β-CD (TB)have been determined by single crystal X-ray structure analysis. Due to the lack of O2···O3‘ hydrogen bonds between adjacent glucose units of the peracylated CDs, the macrocycles are elliptically distorted into nonplanar boat-shaped structures. The glucose units are tilted with respect to the O4 plane to relieve steric hindrance between adjacent acyl chains. In TB, all glucose units adopt the common 4C1-chair conformation and one butanoyl chain intramolecularly penetrates the cavity, whereas, in TA and TP, one glucose unit each occurs in OS2-skew-boat conformation and one acyl chain closes the O6 side like a lid. In each of the three homologous molecules the intramolecular self-inclusion and lidlike orientation of acyl chains forces the associated O5−C5−C6−O6 torsion angle into a trans-conformation never observed before ...
TL;DR: In this paper, a composite model of motion in the system, with contributions both from internal jumping between enantiomeric structures and from overall molecular librations, yields the smallest variance between predicted and measured values.
Abstract: The principal values of the 13C chemical-shift tensor (CST) for biphenyl have been determined with the FIREMAT experiment. The internal dihedral angle between the benzene rings in biphenyl is estimated to fall between 10 and 20° on the basis of quantum mechanical calculations of the CST principal values. A composite model of motion in the system, with contributions both from internal jumping between enantiomeric structures and from overall molecular librations, yields the smallest variance between predicted and measured values for an internal twist angle of 15° between the rings and a mean libration angle of ±12° from the most favored molecular orientation. The composite model is clearly preferred to a motionless model (with >98% probability) and is also preferred over either of the isolated contributing dynamics, i.e., only libration or only internal jumping.
TL;DR: The recent observation, that the Raman basis spectra of oligopeptides have bandwidths significantly narrower than those observed for proteins, may simply result from a side-chain dependence of the amide Raman band frequencies or from a narrow distribution of peptide band geometry.
Abstract: Peptide and protein UV Raman spectra excited at ∼200 nm show strong enhancement of the peptide backbone amide I, II, and III and (C)CR-H vibrations.1-4 We recently demonstrated that these spectra could be analyzed to quantitatively determine secondary structure by modeling the measured spectra with a linear combination of basis spectra of the different secondary structure motifs.4 These Raman studies also demonstrated that the amide III vibration is the most sensitive to peptide conformation; for example, the amide III frequency shifts from 1235 cm-1 in the -sheet to ∼1300 cm-1 in the R-helix conformation.1-4 Since our recent investigations of the UV Raman spectra of peptides indicate that the vibrations of individual peptide bonds are in general uncoupled,5 it may be possible to approximate protein Raman spectra as the linear sum of the spectra of individual peptide bonds. To test this possibility we need to know the dependence of the individual peptide bond Raman spectra on local secondary structure, as well as on their side chain identity and geometry. Our recent observation, that the Raman basis spectra of oligopeptides have bandwidths significantly narrower than those observed for proteins, may simply result from a side-chain dependence of the amide Raman band frequencies or from a narrow distribution of peptide band geometry.6 As previously suggested this dependence could result from either an involvement of side-chain atom motion to the amide III vibrational normal coordinate or a side-chain dependence of the amide bond conformation.7 Some of the earliest studies of amide vibrations empirically demonstrated a strong amide III frequency dependence on the Ramachandran Ψ angle.8 In addition, the experimental results of Williams et al.9,10and theoretical calculations showed an amide III frequency dependence on the Ramachandran Φ angle. They calculated the amide I and III potential energy distributions and the vibrational frequencies for the -sheet and R-helix conformations of dipeptides. For these conformations, they found no systematic dependence of the frequencies and potential energy distribution on side-chain molecular weight. Instead, they found that the amide III frequency shifts resulted from side-chain conformational preferences for particular dihedral angles. Their calculations demonstrated a Φ angle dependence for the magnitude of the contribution of N-H bending and methine proton bending to the amide III vibrational potential energy distribution. To further investigate the Φ angular dependence of the amide III frequency, we have examined the UV resonance Raman spectra of model dipeptides with side chains which are known to have a span of Φ angle preferences. These Φ angle preferences were calculated from Serrano’s11 recent NMR study of the side-chain Φ angle preference in proteins. It should be pointed out that the Φ angle conformational preferences are mainly determined by the side-chain identity and are independent of whether the side chain occurs in a random coil or in an ordered region of the protein.11 We calculated the average side-chain Φ angle from Serrano’s tables by weighting the different Φ angles by their relative probability of occurrence. We measured the UV Raman spectra of a series of acetylated amino acid esters to prevent obfuscation by a spectral dependence on charged penultimate groups. Figure 1 shows the UV Raman spectra of the amide III bands of different side-chain derivatives Ac-X-OCH3, where X is ala, lys, leu, ile, and val. The amide III frequency in this sequence monotonically downshifts from 1322 to 1313 cm-1. These derivatives should show only a Φ dihedral angle conformational dependence because the amide is not linked to a second amide group, and the penultimate CH3 group is 3-fold symmetric with respect to rotation around the CH3-C(O) bond. As suggested by William et al.,9 the amide III frequency does not depend on the side-chain mass, but linearly depends on the side-chain preferences for particular Φ angles11-14 (Figure 2, diamonds). Ac-ala-OCH3, which has a preference for the least negative Φ angle (-78°), has the highest amide III frequency, while Ac-val-OCH3, which has a preference for the most negative Φ angle (-96°, and prefers the -structure11-14), shows the lowest amide III frequency. The other side-chain data fall between that of ala and val. To support these empirical results, which show a Φ angle dependence of the amide III frequency, and to verify that this dependence does not result from mixing in of side chain atomic motion into the amide III vibration, we applied Gaussian 9815 density functional theory (DFT) calculations at the B3YLP 6-31G* To whom correspondence should be addressed. (1) Dudik, J. M.; Johnson, C. R.; Asher, S. A. J. Phys. Chem. 1985, 89, 3805-3814. (2) Song, S.; Asher, S. A. J. Am. Chem. Soc. 1989, 111, 4295-4305. (3) Holtz, J. S. W.; Holtz, J. H.; Chi, Z.; Asher, S. A. Biophys. J. 1999, 76, 3227-3234. (4) Chi, Z.; Chen X. G.; Holtz J. S. W.; Asher, S. A. Biochemistry 1998, 37, 2854-2864. (5) Mix, G.; Schweitzer-Stenner, R.; Asher, S. A. J. Am. Chem. Soc. 2000, 122, 9028-9029. (6) Lednev, I. K.; Karnoup, A. S.; Sparrow, M. C.; Asher, S. A. J. Am. Chem. Soc. 1999, 121, 8074-8086. (7) Krimm, S.; Bandekar, J. AdV. Protein Chem. 1986, 38, 183-364. (8) Lord, R. C. Appl. Spectrosc. 1977, 31, 187-194. (9) Williams, R. W.; Weaver, J. L.; Lowrey, A. H. Biopolymers 1990, 30, 599-608. (10) Weaver, J. L.; Williams, R. W. Biopolymers 1990, 30, 593-598. (11) Serrano, L. J. Mol. Biol. 1995, 254, 322-333. (12) Blaber, M.; Zhang, X.-J.; Matthews, B. W. Science 1993, 260, 16371640. (13) Chou, P. Y.; Fasman, G. D. Biochemistry 1974, 13, 211-222. (14) Koehl, P.; Levitt, M. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 1252412529. Figure 1. 204 nm excited UV RR spectra of peptides (10 mM, pH 6). The instrumentation is described in ref 6. The samples were measured in a temperature-controlled free-surface flowing stream. An accumulation time of 25 min was used for each spectrum. Spectral resolution was 8 cm-1. 7433 J. Am. Chem. Soc. 2001, 123, 7433-7434
TL;DR: The three-dimensional solution structure of microcin J25, the single cyclic representative of the microcin antimicrobial peptide class produced by enteric bacteria, was determined using two-dimensional 1H NMR spectroscopy and molecular modeling.
Abstract: The three-dimensional solution structure of microcin J25, the single cyclic representative of the microcin antimicrobial peptide class produced by enteric bacteria, was determined using two-dimensional 1H NMR spectroscopy and molecular modeling. This hydrophobic 21-residue peptide exhibits potent activity directed to Gram-negative bacteria. Its primary structure, cyclo(-V1GIGTPISFY10GGGAGHVPEY20F-), has been determined previously [Blond, A., Peduzzi, J., Goulard, C., Chiuchiolo, M. J., Barthelemy, M., Prigent, Y., Salomon, R.A., Farias, R.N., Moreno, F. & Rebuffat, S. (1999) Eur. J. Biochem., 259, 747–755]. Conformational parameters (3JNHCαH coupling constants, quantitative nuclear Overhauser enhancement data, chemical shift deviations, temperature coefficients of amide protons, NH–ND exchange rates) were obtained in methanol solution. Structural restraints consisting of 190 interproton distances inferred from NOE data, 11 φ backbone dihedral angle and 9 χ1 angle restraints derived from the coupling constants and three hydrogen bonds in agreement with the amide exchange rates were used as input for simulated annealing calculations and energy minimization in the program xplor. Microcin J25 adopts a well-defined compact structure consisting of a distorted antiparallel β sheet, which is twisted and folded back on itself, thus resulting in three loops. Residues 7–10 and 17–20 form the more regular part of the β sheet. The region encompassing residues Gly11–His16 consists of a distorted β hairpin, which divides into two small loops and is stabilized by an inverse γ turn and a type I′β turn. The reversal of the chain leading to the Phe21–Pro6 loop results from a mixed β/γ turn. A cavity, in which the hydrophilic Ser8 side-chain is confined, is delimited by two crab pincer-like regions that comprise residues 6–8 and 18–1.
TL;DR: The values of the 13C NMR shifts of the ribose sugar are sufficiently precise to allow for statistical separation of sugar puckering modes and exocyclic torsion angle conformers, based on the canonical equation model formulated in a previous paper.