Theoretical conformational analysis by the positive core potential energy method

A simple combination of quantum mechanical and classical methods appears to lead to a new method for theoretical conformational analysis.     

Theoretical study of the conformational features of triosmium clusters

The article summarizes the results of the study of conformational states of triosmium clusters with organic ligands. Special attention is paid to the structural features of molecular carbonyl cluster complexes with M _n (CO) _m L organic ligands. The effect of the structure surface charge, solvent, cluster crystalline state, and intermolecular and intramolecular interactions on the cluster conformational state is also determined.     

Theoretical conformational study of six-membered cyclic allyl epoxides

Accurate “ab initio” calculations (MP2 method) were performed to outline the conformational profile of a number of six-membered cyclic allyl epoxides differing either in the nature of the cycle fragment (Y) bound to the unsaturation, or in the substitution at the endocyclic carbon bound to the epoxy ring and bridging the epoxy ring with the Y fragment. In particular, we calculated structures 4 (Y=CH₂), 5 (Y=O), 6 (Y=NH), 7 (Y=S), 8 (Y=CF₂), 9 (Y=NH₂ ⁺), 10 (Y=CO), 11 (Y=BH) and 12 (Y=NCOOH), where the fragment of the endocyclic carbon bridging “Y” and the epoxy fragment is either non-substituted (4a – 12a) or bears a methyl side chain trans (4b–12b) or cis (4c–12c) to the epoxidic oxygen. Saturated analogs (Y=O and Y=CH₂) were also computed to test the method and to evaluate the conformational profile in the absence of the unsaturation. Minimum energy conformations were found which differ in the relative position of the Y group and the epoxy oxygen, with respect to a plane containing the epoxy ring carbons and the adjacent saturated endocyclic carbon: they may be on the same side (conformer A) or on opposite sides (conformer B). Conformers A are generally more stable. The conjugation effect of Y with the double bond lowers the barrier between the two conformers to the extent that in a few cases only conformer A is associated with a minimum of energy. On the basis of the elongation of the allylic oxirane C–O bond, we postulated the order of reactivity of epoxides 4–12 in the oxirane ring-opening process, and a mechanism based on the more reactive conformer A. A comparison was also made between MP2 and DFT calculation methods.     

Density functional study of indole–pyrrole heterodimer potential energy hypersurface

A density‐functional study of indole–pyrrole heterodimer potential energy hypersurface (PES) was performed. Eight stationary points were located on the B3LYP/6‐31++G(d,p) PES, three of which correspond to real minima, all of them being characterized with an N? H … π type hydrogen bonding. In two of these minima (the local ones), pyrrole subunit acts as a hydrogen bond proton donor, while the global minimum corresponds to indole–H … π(‐pyrrole) arrangement. Besides the interaction and dissociation energies corrected for BSSE and the monomer relaxation energies and the relevant structural parameters, anharmonic N? H and N? H … π vibrational frequencies were calculated for various N? H oscillators involved in this interaction from the 1‐D DFT vibrational potentials. On the basis of anharmonic vibrational frequency analysis, it was concluded that the two types of N? H … π hydrogen bonded dimers (indole vs. pyrrole being a proton donor) should be distinguishable with spectroscopic methods. Various contributions to the overall anharmonic frequency shifts upon hydrogen bonding were calculated and discussed as well. The charge field perturbation (CFP) technique was employed to study the electrostatic + polarization influence of the proton accepting unit on the N? H(… π) vibrational potential. The second‐order perturbation theory analysis (SOPT) of the Fock matrix (i.e., its Kohn–Sham analog) within the natural bond orbital (NBO) basis, as well as various NBO deletion analyses revealed an essentially one‐directional charge transfer (CT) of a π(C? C) → σ*(N? H) type in the case of all three minima. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

Theoretical conformational study of the molecular structures of some bipyridine cardiotonics

Conformational features of amrinone and milrinone have been examined viaab initio (at STO-3G and 3–21G levels) MO theory. The calculated results suggest twisted structures for both the molecules. The higher barrier to rotation of the pyridine ring and restricted conformational flexibility of milrinone are observed to be two significant factors responsible for its greater cardiotonic activity as compared to that of amrinone.     

An exhaustive conformational analysis of N-acetyl-L-cysteine-N-methylamide. Identification of the complete set of interconversion pathways on the ab initio and DFT potential energy hypersurface

The full conformational space of N-acetyl-l-cysteine-N-methylamide was explored by ab initio (RHF/ 6-31G(d)) and DFT (B3LYP/6-31G(d)) computations. Multidimensional conformational analysis predicts 81 structures in N-acetyl-l-cysteine-N-methylamide, but only 47 relaxed structures were previously determined at the RHF/3-21G level of theory. These structures were now optimized using RHF/6-31G(d) and B3LYP/6-31G(d) approaches. Seven conformational migrations were observed when recalculated at higher level of theory. Besides these major changes, only smaller conformational shifts were operative for the remaining stationary points. The exploration of the whole conformational space of N-acetyl-l-cysteine-N-methylamide, including the transition-state structures allowing the conformational interconversion among the low-energy forms, was analyzed in this study. Our results offer new insights into the influence of polar side chains on the conformational preferences of peptide structures.     

Theoretical conformational analysis of rutin

Abstract  

The structural properties of rutin were determined by using a computational multistep progression. In the first step a stochastic strategy based on a molecular mechanics calculation was adopted to obtain a preliminary screening of the low-energy rutin conformations. The most stable structures obtained by the random conformational search were used as a starting point for an Austin Model 1 (AM1) semiempirical optimization. After this treatment, 16 structures characterized by a more stable frontal in respect to back disposition of the glycosidic chain of rutin were identified. To validate the results found from the stochastic search a molecular dynamics simulation was carried out. The results evidenced the presence of a global minimum highly stabilized by a hydrogen bond between the hydroxyl in the 3′ position of the B ring and the endocyclic oxygen of the rhamnose unit followed by approximately 8 kJ mol⁻¹ less stable local minima with similar energy values. Finally, the reliability of the molecular model was confirmed by comparing the calculated electronic absorption spectrum with that measured on a methanolic rutin solution.     

Theoretical study on the potential energy surface and vibrational energy levels of HXeI

The potential energy surface for the electronic ground state of the HXeI molecule is constructed by using the internally contracted multi-reference configuration interaction with the Davidson correction（icMRCI＋Q）method and large basis sets. The stabilities and dissociation barriers are identified from the potential energy surfaces.The three-body dissociation channel is found to be the dominate dissociation channel for HXeI.Based on the obtained potentials,vibrational energy levels of HXeI are calculated using the Lanczos algorithm.Our theoretical results are in excellent agreement with the available observed values.     

Theoretical investigation of the Na+ + H2 system. I. Ab initio calculations including electron correlations of potential energy hypersurface

An ab initio investigation of the potential energy hypersurfaces of the Na⁺/H₂ system is presented. The calculations have been performed on SCF level and with the inclusion of correlation effects by means of the CEPA-PNO , IEPA-PNO , and PNO-CI methods. The basis set consists of gaussian lobes (12s, 8p, d) on Na and (8s, p) on H. The distance of the Na nucleus to the midpoint of H₂ was varied between 0.0 and 10 bohrs, whereas the region of H? H distances considered was 0.5 to 10 bohrs. The angular dependence of the hypersurface was investigated as well. The system Na⁺/H₂ has an absolute energy minimum for C_2v geometry at R equal approximately 5.0 bohrs and r_HH = 1.40 bohrs.     

Theoretical study of the conformational and electrostatic properties of C4-monosubstituted 2-azetidinones

The conformational preferences and electrostatic properties of 2-azetidinone, 4-(S)-methoxycarbonyl-2-azetidinone and 4-(R)-methyl-2-azetidinone have been studied in gas-phase, aqueous solution and CCl₄ solution using quantum mechanical methods. Gas-phase calculations were performed at the ab initio HF, MP2, and MP4 levels and solvent effects were investigated using a self-consistent reaction-field procedure adapted to the AM1 Hamiltonian. An almost planar arrangement was adopted by the-lactam ring in the three cases, whereas the alkoxycarbonyl side group was found to display a large conformational flexibility. The effects of the different solvents on the electrostatic properties of the three compounds were investigated by following the changes in both molecular electrostatic potentials and induced dipole moments. The resulting electrostatic parameters were used as static reactivity indices to predict the response of the systems to the attack of nucleophilic reagents. Theoretical results were compared with experimental data available on the structure and properties of-lactams. The validity of the method as a predicting tool was critically discussed.     

Theoretical study of the conformational states of triosmium clusters with a chiral pinane ligand

A theoretical study of the conformational state of triosmium clusters with a chiral pinane ligand (μ-H)Os₃(CO)₁₀(μ-ONC₁₀H₁₄) has been performed. The potential curves of internal rotation of organic ligands around the N-C bond in cluster complexes in the crystalline state and in various solvents with continual consideration for the parameters of the latter have been determined. The structures of conceivable conformers and isomers are considered; the factors responsible for their formation and stability are examined. The relations between the conformational and crystalline structures of the cluster and the effect of intra-and intermolecular interactions on its structure are revealed.     

HSCCS自由基势能面的理论研究

在CCSD(T)/6-311G(d,f)//MP2/6-311G(d,f) ZPE水平下,计算得到含有8个异构体和11个过渡态的HSCCS自由基体系势能面,讨论了异构体的结构与稳定性及异构体之间的异构化过程.结果表明异构体m1的能量最低,除m1以外,异构体m2和m3的能量也比较低,在MP2水平上,过渡态TS1的能量比异构体m2仅高3.9kJ/mol,而在CCSD(T)水平上,TS1的能量比m2低14.6 kJ/mol,这说明异构体m2可以迅速转化为能量更低的m1.异构体m3的能量比异构体m1高49.99 kJ/mol,可以推断,在合适的实验条件下可以观测到异构体m1.     

Exploring the potential energy hypersurface of histamine monocation: Tautomerism in gas phase

The potential energy hypersurface of the histamine monocation is determined by ab initio methods at the STO -4G level using analytical gradient techniques. Three transition states and two minima have been found for the N_τ? H tautomer. One of the transition states connects the trans conformational region with a minimum gauche structure, where the proton of the ammonium group is approximately halfway between the N_π of the imidazole group and the N of the ammonium group, but nearer to the N_π. This minimum connects the potential energy surface of the N_τ? H tautomer with the imidazolium one. In the latter region, three transition states and two minima have been found. Critical points are discussed in relation with experimental data and histamine H₂ receptor models.     

Theoretical study of the Si2NO potential energy surface

The structures, spectroscopies, and stabilities of the doublet Si₂NO radical are explored at the density functional theory (DFT) and ab initio levels. Seventeen isomers are located, connected by 26 interconversion transition states. At the CCSD(T)/6‐311+G(2df)//QCISD/6‐311G(d)+ZPVE level, three low‐lying isomers are predicted, that is, one bent species SiNSiO 3 (5.1 kcal/mol) containing the important Si?N triple bonding and two four‐membered ring isomers including cyclic cSiNSiO 1 (0.0) with Si? Si cross‐bonding with C_2v symmetry and puckered cSiNSiO 1′ (11.9) with divalent carbene character. Three low‐lying isomers 1, 1′, and 3 have reasonable kinetic stabilities and might be observable either experimentally or astrophysically. The possible formation strategies of 1, 1′, and 3 in laboratory and in space are discussed in detail. The calculated vibrational frequencies and possible formation processes of 3 are consistent with recent experimental observations. In light of the fact that no cyclic nitrogen‐containing species have been detected in space, two cyclic isomers 1 and 1′ could be promising candidates. Furthermore, the bonding nature of three isomers 1, 1′, and 3 is analyzed. The calculated results are also compared with those of the analogue C₂NO radical. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007