SCSA code: applications on the cyclopeptide renieramide

SCSA is an algorithm designed to get information on molecular conformational properties. The most stable conformers are determined by the homemade SCSA code, performing a multistep systematic conformational search, which involves energy and structure quantum chemical optimizations at low-level and high-level. The SCSA method was employed to analyze the conformational space of the in vacuo cyclopeptide renieramide at AM1 and B3LYP/6-31G(d) levels. Calculations at B3LYP level of the GIAO (13)C NMR chemical shifts were also performed on the final conformers. In fact, to validate the conformational search results experimental and calculated (13)C NMR spectra of renieramide were compared. Slight disagreements observed between experimental and calculated spectra could be attributed to solute-solvent interactions, which were not taken into account in the algorithm proposed here.     

Molecular properties from conformational ensembles. 1. Dipole moments of molecules with multiple internal rotations

We present a novel method for constructing the stable conformational space of small molecules with many rotatable bonds that uses our iterative stochastic elimination (ISE) algorithm, a robust stochastic search method capable of finding ensembles of best solutions for large combinatorial problems. To validate the method, we show that ISE reproduces the best conformers found in a fully exhaustive search, as well as compare computed dipole moments to experimental values, based on molecular ensembles and their Boltzmann distributions. Results were also compared to the alternative molecular dynamics and simulated annealing methods. Our results clarify that many low energy conformations may be required to reproduce molecular properties, while single low energy conformers or ensembles of low energy conformers cannot account for the experimental properties of flexible molecules. Whereas ISE well reproduces conformations that are not separated by very large energy barriers, it has not been successful in reproducing conformations of strained molecules.     

Synthesis and conformational analysis of 6-C-methyl-substituted 2-acetamido-2-deoxy-beta-D-glucopyranosyl mono- and disaccharides

Several 6-C-substituted 2-acetamido-2-deoxy-beta-D-glucopyranosides (beta-D-GlcNAc monosaccharides 1a-3a and 1,4-linked disaccharides 1b-3b) were studied by solution NMR spectroscopy. Conformational analysis of the (6S)- and (6R)-C-methyl-substituted beta-d-GlcNAc monosaccharides indicates that the stereodefined methyl groups impose predictable conformational biases on the exocyclic C-5-C-6 bond, as determined by (1)H-(1)H and (13)C-(1)H coupling constants. Variable-temperature NMR experiments in methanol-d(4) were performed to determine DeltaDeltaH and DeltaDeltaS values derived from the two lowest energy conformers. These indicate that while the influence of 6-C-methyl substitution on conformational enthalpy is in accord with the classic principles of steric interactions, conformational preference in solution can also be strongly affected by other factors such as solvent-solute interactions and solvent reorganization.     

Application of J(C,H) coupling constants in conformational analysis

Conformational equilibria for a number of methyl substituted 1,3-dioxanes 1, 1,3-oxathianes 2 and 1,3-dithianes 3 were calculated at the HF and DFT levels of theory. In addition to the chair conformers also the energetically adjacent twist conformers were considered and the positions of the corresponding conformational equilibria estimated. On the basis of the global energy minima of conformers, participating in the conformational equilibria, the ¹J_C,Hax,equ coupling constants were calculated using the GIAO method and compared with the experimental values obtained from ¹³C,¹H coupled ¹³C NMR spectra. The Perlin effect, the influence of the solvent and the suitability of this NMR parameter for assigning the conformational equilibria present are critically discussed.     

Synthesis and conformational analysis of novel N(OCH3)-linked disaccharide analogues

N(OMe)-linked disaccharide analogues, isosteric to the corresponding natural disaccharides, have been synthesized by chemoselective assembly of unprotected natural monosaccharides with methyl 6-deoxy-6-methoxyamino-alpha-D-glucopyranoside in an aqueous environment. The coupling reactions were found to be chemo- and stereoselective affording beta-(1-->6) disaccharide mimics when using Glc and GlcNAc; in the case of Gal, the beta-anomer was prevalent (beta:alpha=7:1). An iterative method for the synthesis of linear N(OMe) oligosaccharide analogues was demonstrated, based on the use of an unprotected monosaccharide building block in which an oxime functionality at C-6 is converted during the synthesis into the corresponding methoxyamino group. The conformational analysis of these compounds was carried out by using NMR spectroscopy, ab initio, molecular mechanics, and molecular dynamics methods. Optimized geometries and energies of fourteen conformers for each compound have been calculated at the B3LYP/6-31G* level. Predicted conformational equilibria were compared with the results based on NMR experiments and good agreement was found. It appears that N(OMe)-linked disaccharide analogues exhibit a slightly different conformational behavior to their parent natural disaccharides.     

SCRF-DFT and NMR comparison of tetracycline and 5a,6-anhydrotetracycline in solution

A combination of structures, energies, and spectral data calculated using density functional theory (DFT) with experimental NMR data has been used to assign conformational equilibria for tetracycline and 5a,6-anhydrotetracycline in water at pH 1, 7, and 10 and in chloroform (5a,6-anhydrotetracycline) and methanol (tetracycline). The results suggest that tetracycline always prefers the extended conformation but that 5a,6-anhydrotetracycline exists in water as a mixture of the two conformers and in chloroform exclusively in the twisted conformation. The conformational equilibria are also shown to be pH dependent.     

Conformational Control of the Electronic Properties of an α‐β Terthiophene: Lessons from a Precursor Towards Dendritic Hyperbranched Oligo‐ and Poly‐Thiophenes

Herein we investigate the conformational and electronic properties of the 2,2′;3′,2“‐terthiophene ( B3T ) unit as the building block of thiophene dendrimeric materials. By means of DFT ground electronic state dihedral energy profiles, we get insight in the flexibility of B3 T as the prominent feature promoting the 3D arrangement. The presence of diverse conformers is explored by Raman and ¹H NMR spectroscopies. A theoretical estimation of the Raman and ¹H NMR spectra over the most energetically accessible conformers is found to be crucial for the appropriate assignment of the major conformer population derived from the experimental spectra. We show that energy barriers for the interconversion of conformers also play a role. Finally, the impact on the optical spectra (absorption and emission) of the α–α and α–β connections is studied and addressed by scanning the properties of the relevant low‐lying excited states. These studies highlight the relevance of the architecture of the basic molecular unit to understand charge and exciton behavior in organic semiconductors, particularly for those useful in photovoltaics.     

Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations

We present a CHARMM Carbohydrate Solution Force Field (CSFF) suitable for nanosecond molecular dynamics computer simulations. The force field was derived from a recently published sugar parameter set.1 Dihedral angle parameters for the primary alcohol as well as the secondary hydroxyl groups were adjusted. Free energy profiles of the hydroxymethyl group for two monosaccharides (beta-D-glucose and beta-D-galactose) were calculated using the new parameter set and compared with similar force fields. Equilibrium rotamer populations obtained from the CSFF are in excellent agreement with NMR data (glucose gg:gt:tg approximately 66:33:1 and galactose gg:gt:tg approximately 4:75:21). In addition, the primary alcohol rotational frequency is on the nanosecond time scale, which conforms to experimental observations. Equilibrium population distributions of the primary alcohol conformers for glucose and galactose are reached within 10 nanoseconds of molecular dynamics simulations. In addition, gas phase vibrational frequencies computed for beta-D-glucose using this force field compare well with experimental frequencies. Carbohydrate parameter sets that produce both conformational energies and rotational frequencies for the pyranose primary alcohol group that are consistent with experimental observations should allow for increased accuracy in modeling the flexibility of biologically important (1-6)-linked saccharides in solution.     

Structure, modelling and dynamic behaviour of aza- and azaoxamacrocyclic ligands derived from (R,R)-1,2-diaminocyclohexane

Investigations into the conformational behaviour of macrocyclic ligands 5 and 6 derived from (R,R)-1,2-diaminocyclohexane have been undertaken using molecular modelling, single crystal X-ray diffraction and variable temperature 1H NMR spectroscopy. These have revealed that the lowest energy conformers in both cases do not possess the expected C2-element of symmetry, which can only be accessed at higher temperatures. Instead both molecules exist as C1-conformers at room temperature and in the solid state. In solution a range of dynamic exchange processes is observed which result, in part from the inherent strain in these fused bicyclic systems. An unexpected but characteristic feature of the C1-symmetric conformers is highlighted by the presence of a signal at unexpectedly low field in their 1H NMR spectra due to the interaction of two of the sulfonyl oxygen atoms with one of the bridgehead hydrogen atoms.     

Calculated chemical shifts as a fine tool of conformational analysis: an unambiguous solution for haouamine alkaloids

In this study, for the first time, conformational analysis by calculated chemical shifts (CCS) deals with a real conformational problem of a large biomolecule. This new methodology is applied to haouamine A, which is much more stereodynamically puzzled than the small models used to validate previous CCS-based conformational studies. Thorough NMR experiments by Zubia et al. on this exotic polyfunctional paracyclophane alkaloid could not determine which experimentally detected interconversion of this compound occurs in solution, rotation or N-inversion. The present study uses CCS to locate the lowest energy conformers and thus to identify the observed stereodynamic process. Molecular mechanics calculations were used to explore the conformational space of this polycyclic system, and then the geometry of located conformers was refined by ab initio calculations at the B3LYP/6-31G(d,p) level; an implicit model for acetone solution was employed. Calculated relative energies are considered too inaccurate to identify the lowest energy (i.e., those detectable by NMR) conformers. Instead, rational regression analysis of CCS for carbon atoms using B3LYP/6-31+G(d)//GIAO-based calculations singled out two conformers from a large set of alternative low energy structures, although solvation shell was not explicitly included in the model. For only these two conformers, the differences in CCS (Delta delta) for selected pairs of carbons are very similar to the experimental Delta delta values. Thus, the conformers monitored by NMR have now been identified; their piperideine ring is of (1)Sf and Sf 1 (sofa-shaped) geometry. This azacycle appears to be flexible despite the presence of the ethylenebiphenylene bridge in haouamines. Interconversion between the conformers probably occurs via a concerted process of inversion of the piperideine ring, N-inversion coupled with rotation around the C-N bond, and rotation around two C-C bonds in the ethylenebiphenylene bridge. This CCS method of conformational analysis is sufficiently simple and reliable that if chemical shifts for a pair of the same carbons are sufficiently different in routine (13)C NMR spectra of stereoisomers (ca. > or = 2 ppm), the "resolving power" of the CCS technique may rival that of NMR techniques.     

蒙特卡洛模拟退火与距离限制相结合的方法——在多肽溶液构象分析中的应用

Distance geometry and molecular dynamics are currently employed in determining molecular structures with interatomic distances from NMR NOESY experiment. Because of the flexibility of peptide, distances obtained from NMR are usually not sufficient to confine its structure. Both distance geometry and molecular dynamics will bias in the conformational space at this circumstance. Constraint Monte Carlo simulated annealing was established to solve this problem. Distance constraints were included into the ECEPP/2 force field by introducing a harmonic energy term. Conformational analysis of a pentapeptide with eight interatomic distances from NMR was carried out as a test. By comparison of the 100 conformers obtained from constraint simulated annealing and the 100 conformers from distance geometry calculation, it was found that constraint simulated annealing can cover the outcomes of distance geometry and at the same time give more con-formers fitting to the experimental data. The result shows that constraint Monte-Carlo simulated annealing is more valid in constructing peptide structures from NMR distances than currently employed methods when no sufficient distances from NMR are available.     

Conformational analyses of peptides and proteins by vibrational Raman optical activity

Recent developments of vibrational Raman optical activity (ROA) spectroscopy enabled the detailed analyses of the backbone and side chain conformations of peptides and proteins in solution phases. ROA can be used as a powerful analytical technique for determining not only the structures of conformers, but also their populations even for systems in fast conformational equilibria where NMR spectroscopy is difficult to be applied. ROA enabled the monitoring of the secondary structures of denatured or unfolded proteins, such as an amyloid fibril and its prefibril intermediates.     

Conformational dynamics in nitrogen-fused azabicycles

Using molecular mechanics (MM3 force field)-based methodology, conformational dynamics have been studied for 1-azabicyclo[2.2.0]hexane, 1-azabicylo[3.3.0]octane, and 1-azabicylo[4.4.0]decane. Obtained conformational schemes describe the flexibity of these parent azabicyles as well as permit us to estimate conformational mobility in related N-fused systems. Quantum mechanics ab initio calculations have been used in order to check the reliability of molecular mechanics-provided estimates of relative energy of conformers. The previous dynamic NMR (DNMR) data have been reinterpreted for some polycyclic alkaloids.     

Conformational analysis of N-Boc-N,O-isopropylidene-α-serinals. A combined DFT and NMR study

This work describes an extensive conformational analysis of Garner's aldehyde and its α-methylated homologue—two important chiral building blocks that are widely used in organic synthesis. A combination of density-functional theory and NMR spectroscopy confirmed the existence of a dynamic equilibrium between two possible conformers of the carbamate group in these compounds. The calculated properties such as conformer populations and rotational barriers around the (CO)-N bond are in good agreement with the experimental values. Finally, the dipole moments of the molecules appear to be a decisive factor in the stabilization of the conformers in solution.     

Hyperconjugation and the increasing bulk of OCOCX3 substituents in trans-1,4-disubstituted cyclohexanes destabilize the diequatorial conformer

The trans diesters of 1,4-cyclohexanediol with a number of acetic acid analogues, CX3COOH, of varying steric hindrance and polarity (CX3 = Me, Et, iso-Pr, tert-Bu, CF3, CH2Cl, CHCl2, CCl3, CH2Br, CHBr2, CBr3) were synthesized, and the axial,axial/equatorial,equatorial conformational equilibria were studied by low-temperature 1H NMR spectroscopy in CD2Cl2. The structures and relative energies of the axial,axial and equatorial,equatorial conformers were calculated at both the MP2/6-311G* and the MP2/6-311+G* levels of theory, and it was only by including diffuse functions that a good correlation of deltaG(o)calcd vs deltaG(o)exptl could be obtained. Both the structures and the energy differences of the axial,axial and equatorial,equatorial conformers are discussed with respect to the established models of conformational analysis, viz., steric 1,3-diaxial and hyperconjugative interactions. Interestingly, the hyperconjugative interactions sigma(C-C)/sigma(C-H) --> sigma*(C-O), together with a steric effect which also destabilizes the equatorial,equatorial conformers on increasing bulk of the substituents, proved to dominate the position of the conformational equilibria. In addition, the preference of the axial,axial conformers with respect to their equatorial,equatorial analogues was greater than expected from the conformational energies of the corresponding substituents in the monosubstituted cyclohexyl esters. The reason for this very interesting and unexpected result is also discussed.     

Design, synthesis, and conformational dynamics of a gated molecular basket

We have developed a synthesis and examined the conformational behavior and recognition properties of dynamic molecular containers 1-3. As follows from the 1H NMR dilution, diffusion NMR, and vapor pressure osmometry measurements, compound 1 has a low affinity for intermolecular aggregation and is mostly present in monomeric form in dilute chloroform solutions. Inspecting the O-H chemical shift resonances of 1, 3, and model compound 4 as a function of temperature afforded the deltadelta/deltaT coefficients of 17.0, 17.3, and 4.7 ppb K(-1), respectively. In combination with the results from variable temperature 1H NMR and IR measurements, the existence of conformers of 1 and 3 in equilibrium, each having a different extent of hydrogen bonding, was confirmed. Molecular mechanics calculations suggested 1a as the most favorable conformation, with three additional conformers, 1b, 1c, and 1d, populating local energy minima. Further optimization of each of the four conformers using semiempirical PM3 and ab initio (HF/6-31G) methods allowed a determination of their relative free energies and the corresponding Boltzmann population distributions which were heavily weighted toward 1a. A computed composite IR spectrum of a fraction-weighted mixture of the conformers of 1 reproduced the experimentally observed IR spectrum in its structural features, leading to a conclusion that conformer 1a indeed dominates the equilibrium. The egg-shaped cavity of 1 (136.6 angstroms3) is complementary in size, shape, and electrostatic potential to chloroform (74.9 angstroms3). A single-crystal X-ray study of 2 revealed a disordered chloroform molecule positioned inside the cavitand along its C3 axis.     

RNA unrestrained molecular dynamics ensemble improves agreement with experimental NMR data compared to single static structure: a test case

Nuclear magnetic resonance (NMR) provides structural and dynamic information reflecting an average, often non-linear, of multiple solution-state conformations. Therefore, a single optimized structure derived from NMR refinement may be misleading if the NMR data actually result from averaging of distinct conformers. It is hypothesized that a conformational ensemble generated by a valid molecular dynamics (MD) simulation should be able to improve agreement with the NMR data set compared with the single optimized starting structure. Using a model system consisting of two sequence-related self-complementary ribonucleotide octamers for which NMR data was available, 0.3 ns particle mesh Ewald MD simulations were performed in the AMBER force field in the presence of explicit water and counterions. Agreement of the averaged properties of the molecular dynamics ensembles with NMR data such as homonuclear proton nuclear Overhauser effect (NOE)-based distance constraints, homonuclear proton and heteronuclear ¹H–³¹P coupling constant (J) data, and qualitative NMR information on hydrogen bond occupancy, was systematically assessed. Despite the short length of the simulation, the ensemble generated from it agreed with the NMR experimental constraints more completely than the single optimized NMR structure. This suggests that short unrestrained MD simulations may be of utility in interpreting NMR results. As expected, a 0.5 ns simulation utilizing a distance dependent dielectric did not improve agreement with the NMR data, consistent with its inferior exploration of conformational space as assessed by 2-D RMSD plots. Thus, ability to rapidly improve agreement with NMR constraints may be a sensitive diagnostic of the MD methods themselves.