Ab initio conformational analysis of cyclooctane molecule

The potential energy surface (PES) for the cyclooctane molecule was comprehensively investigated at the Hartree–Fock (HF) level of theory employing the 3–21G, 6–31G, and 6–31G* basis sets. Six distinct true minimum energy structures (named B, BB, BC, CROWN, TBC, and TCC₁), characterized through harmonic frequency analysis, were located on the multidimensional PES. Two transition state structures were also located on the PES for the cyclooctane molecule. Electron correlation effects were accounted for using the Møller–Plesset second-order perturbation theory (MP2) approach. The predicted global minimum energy structure on the ab initio PES for the cyclooctane molecule is the BC conformer. A gas phase electron diffraction study at 300 K suggested a conformational mixture while an NMR study in solution at 161.5 K predicted the BC conformer as the predominant form. The equilibrium constants reported in the present study, which were evaluated from the ab initio calculated total Gibbs free energy change values, were in good agreement with both experimental investigations. The ab initio results showed that the low temperature condition significantly favored the BC conformer while above room temperature both BC and CROWN structures can coexist. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 524–534, 1998     

Ab initio study of the conformational equilibrium of ethylene glycol

Summary The conformational equilibrium of ethylene glycol (CH₂OHCH₂OH) has been examined by performing geometry optimizations at the 6-31G*, MP2/6-31G* and 6-31G** levels. Final energies have been calculated at the MP3 level with the optimized geometries. The two most stable conformers are atGg andgGg but it is verified that the inclusion of electronic correlations reduces their energy difference of 0.6 kcal/mol at the HF level to less than 0.2 kcal/mol. The possible coexistence of the two most stable conformers is in agreement with some previous studies of Frei et al. For thetXg conformer a detailed analysis of the intramolecular potential as a function of rotation around the C-C bond is also reported.     

Ab initio studies of conformational properties of dimethyl diphosphate dianion and its complex with magnesium

The conformational properties of the diphosphate linkage have been studied with ab initio methods using the dimethyl diphosphate dianion (1) and magnesium dimethyl diphosphate (2) as models. The ab initio energy and geometry of the conformers around the P-O bonds have been determined at the self-consistent-field (SCF) using the 6-31G* and the tzp basis sets; whereas, the 6-31G* basis set alone has been used for 2. In addition, the adiabatic connection method (ACM) of density functional theory (DFT) using the dzvp basis set has been employed for 1. The optimization of all possible staggered conformers assumed for the four P-O bonds, led to nine minima for 1. In agreement with the general anomeric effect, the sc conformation about the P-O bonds is clearly preferred over the ap one. Vibrational frequencies were calculated at the SCF level using the 6-31G* basis set and used to evaluate zero-point energies, thermal energies, and entropies for all minima of 1. The effect of zero-point energies and thermal energies is quite small. However, the effect of entropies, mainly resulting from a multiplicity contribution, changes the stability of the conformers. For each minimum of 1, up to six different arrangements of the Mg²⁺ were used to determine minima of 2. This procedure led to 21 distinct minima. The presence of the magnesium counter-ion appeared to completely change the structure and relative energy of the conformers. The preferred structures of the complex exhibit the (sc, ap) orientation around the two central P–O bonds and an arrangement in which the magnesium cation is coordinated by three phosphoryl oxygen atoms. The results of this work clearly demonstrate that interactions with the metal counter-ion can induce conformational changes in the overall 3D-shape adopted by molecules containing diphosphate linkages. The PM3 and MNDO quantum semi-empirical methods and molecular mechanics methods using the CVFF force field were tested and large differences in the minimum structures, as well as in the conformational energies between these and ab initio methods, are discussed.     

Ab initio conformational maps in the gas phase and aqueous solution for a prototype of the glycosidic linkage

Ab initio conformational maps for methoxyethoxymethane (MEM) in both the gas phase and aqueous solution have been constructed using two different approaches. The results obtained allow us to conclude that a rigid conformational map is able to predict the regions of the minima, in the potential energy surface of MEM, in full agreement with those found in the relaxed conformational map, in both phases studied. This is a good indication that ab initio rigid conformational maps may be reliably used to sort the stablest conformers of disaccharides in aqueous solution. Besides that, in the MEM case, the solvation effects do not give rise to any new local minimum in its potential energy surface, but just change the relative energies of the stablest conformers found in the gas phase. This may be an indication that even in aqueous solution the anomeric effect is still the determinant effect defining the conformation of the molecule.Proceedings of the 11th International Congress of Quantum Chemistry satellite meeting in honor of Jean-Louis Rivail     

Ab initio studies of the conformers and conformational distribution of the gaseous hydroxyamino acid threonine

Systematic and extensive conformational search has been performed to characterize the gas-phase threonine structures. A total of 1296 unique trial structures were generated by allowing for all combinations of internal single-bond rotamers. All the trial structures were optimized at the B3LYP/6-311G* level of the theory and then subjected to further optimization at the B3LYP/6-311++G** level. A total of 71 conformers were found and their rotational constants, dipole moments, zero-point vibrational energies, harmonic frequencies and vertical ionization energies of all the conformers were determined. Single-point energies were also calculated at the MP2/6-311G(2df,p) and B3LYP/6-311G(2df,p) levels. Characteristic H-bonding types were classified and listed for all the conformers. The conformational distributions of gaseous threonine at various temperatures were calculated.     

WIZARD: AI in conformational analysis

Summary A program which utilizes the techniques of Artificial Intelligence and Expert Systems to solve problems in the area of Conformational Analysis is described. The program searches conformational space in a systematic fashion, based on the technique known as heuristic state-space search. The program proceeds by recognizingconformational units, assigning one or moreconformational templates to each unit, andjoining them to form conformational suggestions. These suggestions arecriticized to discover logical inconsistencies, and any resulting stresses areresolved. The resulting conformational suggestions are sometimes accurate enough for immediate use, or may be further refined by a numerical program. The latter combination is shown to be quite efficient compared to purely numerical conformational search techniques.     

Ab initio studies on the vibrational spectra and conformational isomerism of 2,4-dimethyl-1,3-pentadiene

Ab initio was used to study the structure of various conformational isomers and their vibrational spectra of 2,4-dimethyl-1,3-pentadiene (2,4-PD) in detail. Two stable conformations, s-trans and s-cis, were found in which s-trans is more stable. The geometry of stable conformations and charge distributions were studied, and the effect of different basis sets on geometry optimization is discussed. The results of complete optimization indicate that molecular skeleton is nearly in a plane, its largest deviation is only 0.3 degrees. Therefore, it is reasonable and available to hypothesis that the molecule has Cs symmetry. The thermal dynamics conformations were calculated and compared with experimental values. DeltaH(o) between two conformations of 2,4-PD measured from experiment is 4.36 kJ/mol, deltaS(o) is 2.56 J/mol K., calculated results are slightly different from experimental ones. Vibrational frequencies of 2,4-PD conformers have been studied by ab initio molecular orbital calculations using different basis set. The calculated vibrational frequencies are analyzed and compared with the experimental spectra.     

Ab initio analysis of the conformational changes of the prolyl-proline model peptide

For- -Pro- -Pro-NH₂ is an ab initio model of the prolyl-proline sequence unit present in numerous peptides and proteins. Cis–trans isomerization of the peptide linkage is a crucial step in accessing the active conformation of several proline containing macromolecules.

The present study focuses on the flexibility of the five-membered pyrrolidine ring, which is considered to help other conformational changes as well as cis–trans isomerization. Ring flexibility is characterized by the pseudorotational amplitude, A, and the phase angle, P. Calculations are carried out at the RHF/6-31+G(d) level of theory. The choice of method and level of theory is further supported by single point DFT calculations.

In the course of NMR structure determination of peptides or proteins, proline residues present in the sequences need special attention. Because of the lack of an amide hydrogen, sequential assignment of proline is rather complicated. Furthermore, in solution state, peptide cis–trans isomers are almost always present. Ab initio study on the For- -Pro- -Pro-NH₂ model is a useful tool to discover the structural characteristics of the prolyl-proline sequence unit.     

Conformational Analysis of 2,2′-bifuran: Correlated High-level Ab initio and DFT Results

The torsional potential for inter-ring rotation in 2,2′-bifuran has been systematically tackled using highly accurate ab initio calculations as well as cost-effective DFT methods. The successful convergence of the ab initio results allowed to confirm the presence of a shallow gauche minimum in the torsional potential curve. The standard DFT methods failed to capture such a tiny energy barrier but, interestingly, the results could be remarkably improved by a mixture of wavefunction and DFT energies in a multi-coefficient fashion; thus, accurate DFT-based and ab initio reference data also become available. Since the experimental evaluation of torsional potentials faces quantitative problems, the outcome of high-level theoretical calculations is expected to be reliably used in further investigation on structure and conformational distribution of this system.     

Comparative conformational analysis of peptide T analogs

A series of peptide T analogs were investigated within the molecular mechanics framework. In order to determine the role of the aminoacid residues in spatial formation of peptide T the conformational peculiarities of the glycine-substituted analogs were investigated. The conformational profiles of some biologically tested analogs of this peptide were determined independently. The received data permit to assess the active form of this peptide. It is characterized by β-turn at the C-terminal physiologically active pentapeptide fragment of peptide molecule. The received results are important for the investigation of the structure-activity relationship and may be used at design of a rigid-molecule drug against HIV.     

Gas phase and water solution conformational analysis of the herbicide diuron (DCMU): an ab initio study

In the present work, the conformational equilibrium for the herbicide diuron (DCMU) has been investigated using high level ab initio calculations. The solvent effect was included through two different continuum models: (1) the real cavity IPCM method and (2) the standard dipole Onsager model SCRF. The effect due to solute-solvent hydrogen-bond interactions was analyzed considering a hybrid discreet-continuum model. At the Hartree-Fock level, the gas phase results showed that only the trans forms (A and B) are present in the equilibrium mixture, with the relative concentrations found to be 33% (A) and 67% (B) (HF/6-311+G**//6-31G**). When the electronic correlation effect is included (MP2/6-31G*//HF/6-31G*), a relative stabilization of the cis forms was observed, with the conformational distribution calculated as 38% (A), 50% (B), 6% (C) and 6% (D). The trans conformations were found to be completely planar, which has been considered to be a prerequisite for the herbicide binding. In water solution, the trans conformation A should be the most abundant conformer, the IPCM and SCRF values being ca. 100% and ca. 85% respectively. The IPCM calculations with the isodensity level set to 0.0005 present a conformational distribution close to that obtained from the hybrid model [92% (A) and 8% (B)], which has been considered our best solvent approach. Regarding the biological action of urea-type herbicides, the results presented here are important, because some QSAR studies have suggested that the partition coefficient is related to the herbicide activity, so the conformational equilibrium may play a role in the biological action. Received: 23 February 1998 / Accepted: 28 May 1998 / Published online: 19 August 1998     

Esters of 2,5-multisubstituted-1,3-dioxane-2-carboxylic acid: their conformational analysis and selective hydrolysis

The carbomethoxy group at the C2 position of the 2,5-multisubstituted 1,3-dioxanes prefers the axial conformation rather than the equatorial one due to an anomeric effect. The trans isomers of the 5-monosubstituted compounds are more selectively hydrolyzed than the cis isomers. Based on the calculated results, hydrolysis to the trans isomers is attributed to the larger carbonyl charges of the trans than those of the cis isomers. The anomeric and homoanomeric effects will explain the axial preference of the carbomethoxy group and selective hydrolysis to the trans isomers. Furthermore, the calculated stability between the cis and trans isomers is in good agreement with the experimental results in the equilibrium state.     

Vibrational analysis of a rate-slowing conformational kinetic isotope effect

An enthalpy-entropy approach to analyzing a rate-slowing conformational kinetic isotope effect (CKIE) in a deuterated doubly-bridged biaryl system is described. The computed isotope effect (k_H/k_D?=?1.075, 368?K) agrees well with the measured value (k_H/k_D?=?1.06, 368?K). The rate-slowing (normal isotope effect) nature of the computed CKIE is shown to originate from a vibrational entropy contribution defined by the twenty lowest frequency normal modes in the ground state and transition state structures. This normal entropy contribution is offset by an inverse vibrational enthalpy contribution, which also arises from the twenty lowest frequency normal modes. Zero point vibrational energy contributions are found to be relatively small when all normal modes are considered. Analysis of the H_ZPE, H_vib, and S_vib energy terms arising from the low frequency vibrational modes reveals their signs and magnitudes are determined by larger vibrational energy differences in the labeled and unlabeled ground state structures.     

Conformational analysis of melatonin at Hartree–Fock ab initio level

Melatonin is a hormone, which is synthesized and secreted by the pineal gland during darkness and has been implicated in the regulation of several neural and endocrine processes. Conformational analysis of melatonin was performed at Hartree–Fock ab initio level. With the help of STO-3G and 6-31G* basis sets, 192 and 128 conformers were obtained, respectively. In both cases, there were eight conformers with nearly planar 3-amido-side chain and the most stable conformation found had folded structure in accord with previously published results. The present paper compares the Hartree–Fock conformational space of melatonin with the results of active conformation models and conformational analyses published in the literature.     

Ab initio molecular dynamics of liquid 1,3-dimethylimidazolium chloride

Density-functional-based Car-Parrinello molecular dynamics (CPMD) simulations have been performed for the ionic liquid 1,3-dimethylimidazolium chloride, [dmim]Cl, at 438 K. The local structure of the liquid is described in terms of various partial radial distribution functions and anisotropic spatial distributions, which reveal a significant extent of hydrogen bonding. The cation-anion distribution simulated with the BP86 functional is in qualitative agreement with the structural model derived from neutron diffraction data for the liquid, whereas the theoretical cation-cation distribution shows less satisfactory accord. Population analyses indicate noticeable charge transfer from anions to cations, and specific CH...Cl hydrogen bonds are characterized in terms of donor-acceptor interactions between lone pairs on Cl and antibonding sigma(CH) orbitals.     

99mTc complexes of 1,3-propanedithiol derivatives

The labelling of 1,3-n alkylpropanedithiols and of 15-/1,3-dimercapto 2-propyl/ pentadecanoic acid by^99mTc has been performed by an exchange reaction with the hexachlorotechnetate ion^99mTcCl ₆ ^2– and by reduction of^99mTcO ₄ ^– with Sn/II/ in the presence of the ligand. The biological distribution of the exotechnetium complexes obtained by the latter method in mouse does not reveal a high tropism of these labelling compounds in relation to a particular tissue.     

Synthesis and conformational analysis of new naphth[1,2-e][1,3]oxazino[3,4-c]quinazoline derivatives

A new highly functionalized aminonaphthol derivative, 1-(amino(2-aminophenyl)methyl)-2-naphthol (4), was synthesized by the reaction of 2-naphthol, 2-nitrobenzaldehyde and tert-butyl carbamate or benzyl carbamate, followed by reduction and/or removal of the protecting group. The aminonaphthol derivative thus obtained was converted in ring-closure reactions with formaldehyde, benzaldehyde and/or phosgene to the corresponding naphth[1,2-e][1,3]oxazino[3,4-c]quinazoline derivatives. The conformational analysis of some derivatives by NMR spectroscopy and accompanying molecular modelling are also reported.     

Ab initio stochastic optimization of conformational and many-body degrees of freedom

Moderate to large size molecules in solution have complex energy surfaces due to intramolecular (conformational) and intermolecular (many-body) interactions. The first principles Monte Carlo (FPMC) method, previously shown to effectively locate minimum-energy structures for systems with only many-body complexity, has been extended to address conformational flexibility by adding three new Monte Carlo move types. The primary advantage of the FPMC method is the ability to efficiently locate minimum energy structures of molecules with conformational flexibility in the presence of explicit solvent molecules using highly accurate quantum chemical calculations. The additions to FPMC were validated by studying conformers of glycerol, glyceraldehyde, and a large humic acid monomer unit. The structure of glyceraldehyde in the presence of one and two water molecules was also explored to demonstrate the power of FPMC to study systems with both conformational and many-body degrees of freedom.     

Ab initio analysis of lithium dimethylaminoborohydride

Ab initio calculations were used to determine the equilibrium geometries and energies of lithium dimethylaminoborohydride. Relative energies of the monomeric and dimeric species were calculated in the gas phase and for the dimethyl ether microsolvated molecules. The most stable structure was a dimer in which the lithium and boron atoms were bridged by two hydrogen atoms, similar to the three-center two-electron bonds in diborane. This hydrogen bridging was maintained in the lithium dimethylaminoborohydride bis(dimethyl ether) microsolvate.