Theoretical investigations on the weak nonbonded CS···CH2 interactions: Chalcogen‐bonded complexes with singlet carbene as an electron donor

In this article, we explored the noncovalent bonding interactions between O?C?S, S?C?S, F₂C?S, Cl₂C?S, and singlet carbene. Six chalcogen‐bonded complexes were obtained. It is found that all the vibrational frequencies of C?S bond presented a red shift character. Interaction energy, topology property of the electron density and its Laplacian, and the donor–acceptor interaction have been investigated. All these results show that there exists a weak nonbonded interaction between the chalcogen bond donor and CH₂. An energy decomposition analysis was performed to disclose that the electrostatic interaction is the main stabilized factor in these nonbonded complexes. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Ab initioSTO-3G optimization of planar,perpendicular, and twisted molecular structures of biphenyl

The complete molecular structure of biphenyl, characterized by 12 independent parameters, has been derived by ab initio gradient techniques using a STO -3G basis set for coplanar, perpendicular, and minimum energy conformations with the constraint of planar phenyl ring units and a C₂ symmetry axis along the CC interring bond. The minimum torsional angle obtained was ? = 38.63° with torsional energy barriers of 8.59 and 10.04 kJ/mol for ? = 0° and ? = 90°, respectively.     

π-Bond Configurations,Conformations, and Dynamic Behaviour of Benzo[c]octalene and Dibenzo[c,j]octalene

The π-bond configurations, the conformations, and the dynamic behaviour of dibenzo [c,j]octalene (2) and of benzo [c]octalene (3) have been investigated by ¹³C-NMR. spectroscopy at different temperatures. Dibenzooctalene was found to present π-bond fixation in the octalene unit as in 2b ; with this π-bond fixation the molecule is not planar and takes two different conformations which are rapidly interconverted by inversion of one cyclooctatetraene ring. Monobenzooctalene (3) also presents π-bond fixation in the octalene unit but exists as two valence isomers, 3b and 3c. Isomer 3c dominates the dynamic equilibrium. With this π-bond configuration, the molecule is chiral but undergoes several isodynamic processes, namely inversion of the cyclooctatriene and/or of the cyclooctatetraene ring. The valence isomer 3b can have two different conformations which are rapidly interconverted by inversion of one cyclooctatetraene ring. The interconversion 3c ? 3b implies the occurrence of a π-bond shift process; this process affects the ¹³C-NMR. lineshape above 50°.     

Efficient algorithm for conformational search of macrocyclic molecules

A new algorithm, complementarity, is developed for conformational search of macrocyclic molecules. The algorithm scans a large number of candidate conformations and energy-minimizes only the promising ones. These candidates can be generated by two operators that construct new conformations from known minima. The candidates have similar bonded-interaction energy as the known minima and possibly lower nonbonded interaction energy. This algorithm is 9 to 11 times faster than the existing methods when tested on two large rings, cycloheptadecane and rifamycin SV. © 1997 by John Wiley & Sons, Inc.     

Photochemische Reaktionen. 68. Mitteilung. Die Photoisomerisierung von α,β-ungesättigten γ,δ-Epoxyketonen: 9α, 10α- und 9β, 10β-Oxido-3-oxo-17β-acetoxy-Δ4-östren

Irradiation in the n→π* absorption band of the α,β-unsaturated γ,δ-epoxyketone 5 in ethanol at ?65° exclusively afforded the rearranged ene-dione 13 , whereas at + 24° under otherwise unchanged reaction conditions or upon triplet sensitization with Michler's ketone and with acetophenone at + 24° essentially identical mixtures of 13 (major product), 14 , and 15 were obtained. Selective π→π* excitation of 5 at ?78° and + 24° led to similar product patterns. The 9β,10β-epimeric epoxyketone 7 selectively isomerized to 14 and 15 at + 24° and n → π* or π → π* excitation. Neither the epoxyketones 5 and 7 nor the photoproducts 13–15 were photochemically interconverted. In separate photolyses each of the latter gave the double bond isomers 16 , 18 , and 19 , respectively. Cleavage of 13 to the dienone aldehyde 17 competed with the double bond shift ( → 16 ) when photolyzed in alcoholic solvents instead of benzene. The selective transformations 5 → 13 (at ?65° and n → π* excitation) and 7 → 14 + 15 are attributed to stereoelectronic factors facilitating the skeletal rearrangements of the diradicals 53 and 55 , the likely primary photoproducts resulting from epoxide cleavage in the triplet-excited compounds 5 and 7 , via the transition states 54 , 56 , and 57 . The loss of selectivity in product formation from 5 at higher temperature and n → π* excitation or triplet sensitization is explicable in terms of radical dissociation into 58 and 59 increasingly participating at the secondary thermal transformations of 53 . The similar effect of π → π* excitation even at ?78° indicates that some of the π,π* singlet energy may become available as thermal activation energy. It is further suggested that the considerably lesser ring strain in 14 and 15 , as compared with 13 , is responsible that selectivity in product formation from 7 is maintained also at +24° and at π → π* excitation.     

A computational investigation and the conformational analysis of dimers, anions, cations, and zwitterions of L-phenylalanine

The structure and stability of various conformations of L-phenylalanine (PheN) and its zwitterions (PheZ), along with their ionized counterparts, cation (PheC) and anion (PheA), generated by adding and removing a proton respectively, have been investigated using first principle calculations in vacuum and in solution. This is followed by an extensive study on various possible dimer (PheD) conformations, which are noncovalently bound units without a peptide bond. This study results in 52, 31, 12, 9, and 11 minimum energy structures on the potential energy surfaces of PheD, PheN, PheC, PheA, and PheZ, respectively. Several important nonbonded interactions such as hydrogen bonds, NH-π, CH-π, OH-π, and π-π interactions, which impart stability to the monomeric and dimeric units, have been analyzed. The capability and strength of the nonbonded interactions drastically changing the conformational orientations of monomeric units has been illustrated.     

Ab initio studies of structural features not easily amenable to experiment. 42. Molecular geometries and conformational analysis of methylbutanoate

Conformational energy profiles were calculated for τ₁, the C? C? C?O torsion, and τ₂, the C? C? C? C torsion, of methyl butanoate, using Pulay's ab initio gradient procedure at the 4-21G level with geometry optimization at each point. In addition, the structures of seven conformations were fully relaxed, including the energy minima (τ₁, τ₂) = (0, ?60), (0, 180), (120, 180), (120, ?60), and the maxima (0, 0), (180, 180), and (60, ?60). The calculated geometries confirm the previously formulated rule that, in saturated hydrocarbons, a C? H bond trans to a C? C bond (C? H_s) is consistently shorter than a C? H bond (C? H_a) trans to another C? H bond. Specifically, for X? C(α) (? O)? C(β)? C(γ)? C(δ) systems, the following rules can be formulated, incorporating results from previous studies of butanal, butanoic acid, and 2-pentanone: (1) C(δ)? H_s < C(δ)? H_a in all the conformers in which the δ-methyl group is remote from the ester group; whereas, in all the conformers in which nonbonded interactions are possible between the C(δ)-methyl and the ester groups, the bonding pattern is affected by a C? H ?O?C interaction. (2) In the most stable conformers, (0, 60), C(β)? H_a < C(β)? H_s, and C(γ)? H_a < C(γ)? H_s, regardless of X. (3) The average C? C bonds in the τ₂ = 180° conformers are consistently shorter than those with τ₂ = 60° (compared at τ₁ constant). In the most stable conformations (τ₁ = 0°, τ₂ = 60° or 180°), the bonding sequence is consistently C(α)? C(β) < C(β)? C(γ) < C(γ)? C(δ); whereas, when τ₁ = 120°, C(α)? C(β) < C(β)? C(γ) > C(γ)? C(δ).     

3,4',5-三甲氧基-1,2-二苯乙烯合成、晶体结构与量子化学研究

利用Wittig-Horner反应制备了抗癌保健药物白藜芦醇的前体化合物3,4',5-三甲氧基-1,2-二苯乙烯, 单晶结构解析结果表明, 该晶体属于三斜晶系, 空间群P1, 晶胞参数: a=0.9960(12) nm, b=1.0040(12) nm, c=1.6194(19) nm, α=90.702(2)°, β=105.515(2)°, γ=111.815(2)°, V=1.6194(3) nm3, Dc=1.249 Mg/m3, 结构基元分子数Z=2. 对晶体结构的结构基元进行了量子化学研究, 计算结果表明, 3,4',5-三甲氧基-1,2-二苯乙烯晶体结构基元与组成结构基元分子两种不同构象能量和的差值为ΔEBSSE=5.51 kJ/mol. 因此,晶体结构基元中两种构象之间存在π-π堆积相互作用.     

Conformational study of halogen- and hydrogen-substituted polythionylphosphazenes using density functional theory method

The structure and conformational stability of polythionylphosphazenes is investigated by modeling single polymer chains with small mimics. The model compounds are composed of repeat units of the corresponding polythionylphosphazenes. Two of the model compounds have hydrogens and two have chlorines as substituents on phosphorus atoms. The substituents on sulfur may be either fluorine or chlorine. Fully geometry-optimized structures and energies of the stable conformations involving rotations around the P? N bond near the sulfur are obtained using the density functional theory method. The structural and conformational analyses indicate that the rotation around the N? P bond leads to variations in the bond lengths, the SNP bond angle openings, as well as couplings between dihedral angles in different conformations in all model compounds. In addition, the conformational analysis suggests that the minima on the conformational potential energy surface in these compounds may be located in the vicinity of the following values of the NP? NS dihedral angle: -50°, 90° (or 60°), 180°, and 240°. It was found that the values of the conformational energy differences range between less than 1 to 5 kcal/mol. A comparison is made between the structural results obtained using the density functional theory and the ab initio molecular orbital theory for the global minimum structures. © 1995 John Wiley & Sons, Inc.     

Ab initio studies of structural features not easily amenable to experiment. 30. Conformational analysis and molecular structures of propanal and butanal

The geometries of several conformations of propanal and butanal have been refined by geometrically unconstrained ab initio gradient relaxation on the 4-21G level. Both compounds possess energy minima at O? C? C? C torsional angles of 0° and in the 120° region, and energy maxima in the 70° region and at 180°. The structure of the aldehyde functional group is found to be relatively invariant both when different systems or when different conformations of the same system are compared. Conformationally dependent geometrical trends in propanal and butanal are discussed and found to be subtle yet noticeable.     

Conformational Flexibility of the Methoxyphenyl Group Studied by Statistical Analysis of Crystal Structure Data

In a large sample of observed methoxyphenyl groups, the twist angle τ about the MeO-C_Ph bond measuring internal rotation of the MeO group shows a continuous distribution with maxima at (0°) (coplanar conformation) and (～90°) (perpendicular conformation). The preferred conformation of methoxyphenyl depends on the nature of the ortho--substituents: In general, it is coplanar in the case of one or two ortho-hydrogens, and perpendicular in the case of two substituents. The internal rotation of the MeO group is accompained by systematic variations in bond angles and bond distances: 1 if MeO is twisted out of plane, the bond angle CH₃? O? C_Ph decreases from 117.7°, until it reaches a minimum of 114.9° at τ = ±90°. The O? C? C angle which is syn to CH₃ for τ = 0° decreases from 124.6° to a minimum of 115.4° at τ = ±180°. These angles changes keep the nonbonded distance CH₃ …? ortho substituent maximal during internal rotation of MeO and tend to minimize the corresponding strain energy. (2) In the perpendicular conformation, the O-atom is ～ 0. 06 Å displaced from the Ph plane, O and CH₃ and being on opposite sides of this plane. In addition, small but systematic increases of bond lengths MeO? C_Ph and CH₃? O are observed. These variations indicate a decrease in conjugation with increasing twist angle. Their interdependence during twisting and the magnitudes of the changes are close values obtained by ab initio calculations.     

Ab initio studies of structural features not easily amenable to experiment. 38. Structural and conformational investigations of propanoic, 2-methylpropanoic,and butanoic acid

The structures and conformational energies of several conformations of propanoic acid, 2-methylpropanoic acid, and butanoic acid were determined by geometrically unconstrained ab initio gradient geometry refinement on the 4-21G level. The O?C? C? C torsional potentials of propanoic acid and butanoic acid are found to be practically identical. There are energy minima at 0° and 120°, and maxima in the 60° region and at 180°. In 2-methylpropanoic acid there are energy minima at H? C? C?O dihedral angles of 0° and 120°, and maxima at 60° and 180°. The exact positions of the maxima and minima of the H? C? C?O torsional potential of 2-methylpropanoic acid are found to be predictable from propanoic acid rotational-potential parameters. Some conformationally dependent, local geometry trends are discussed.     

Concerning the Conformation of Isolated Benzylideneaniline

From PE.-spectroscopical studies the torsional angle φ of the N-phenyl ring in isolated benzylideneaniline 1 has been found to be definitely smaller than φ= 90°. An approximate valueφ= 36°has been estimated which is even smaller than the one observed in the crystal (φ= 55°) and suggested to prevail also in solutions of 1 . A reevaluation of the gas phase optical spectrum of isolated 1 supports a torsional angle similar to that found in the other phases. Calculations of the most stable conformation of 1 as well as of stilbene and azobenzene by the MINDO/3-technique lead to torsional angles φ= 90° for both phenyl rings in all cases. These results are at variance with the experimental results and suggest that MINDO/3-like its less advanced precursor MINDO/2 or like CNDO/2–is unreliable for low energy processes involving rotation of π-systems connected by essential single bonds. It is concluded that the π-energy of benzylideneaniline, like that of stilbene or azobenzene, would favor a planar conformation. The increased torsional angle in 1 as compared to the other two iso-conjugate systems arises from a larger steric interaction between phenyl- and bridgeprotons.     

Role of electron correlation in the quantum-mechanical calculations of the coulomb interaction energy in the DNA base pairs

The intermolecular electronic correlation contributions to the Coulomb component of the nucleic acid base interaction energy are estimated. The Coulomb energy is evaluated with the use of atomic monopoles, which are determined from the π-electronic densities calculated by the SCF method and by employing partially or completely optimized APSG wave functions. When the correlation is thus taken into account, a systematic decrease in atomic charges occurs; this effect is considerable only if an optimized orbital set is used. As a result, the Coulomb interaction energy due to the π-electronic atoms decreases from ?1.13 to ?0.85 kcal/mol for the AT pair and from ?7.15 to ?4.61 kcal/mol for the GC pair.     

Carbonyles tres decales par rapport a l'eclipse dans les aldehydes et les cetones aliphatiques satures: analyse conformationnelle theorique

The theoretical conformational analysis of two series of molecules HCOR, MeCOR is treated. Spectroscopic data [15] have indicated the existence of non-eclipsed conformations which become more important with increasing steric hindrance of the group R.All the methods used (semi-empirical quantum methods, P.C.I.L.O., I.N.D.O., C.N.D.O./2, and the Liquori empirical potential method) lead to the following stable conformations: with the carbonyl group exclusively eclipsed for slightly substituted R (R = Me, Et, tBu); with the carbonyl eclipsed and also staggered (? ? 60°) for moderately substituted compounds (MeCOPr, MeCOiBu, MeCOCiPr(Me)₂) (low rotational barriers permitting equilibria between eclipsed and staggered conformations); with the carbonyl exclusively staggered (? ? 60°) for more hindered compounds (MeCOCH₂tBu, MeCOCH(tBu)Me, MeCOC(Me),tBu, MeCOCH(tBu)₂).Contradictory results are obtained for certain compounds (iPrCOMe, tBuCH₂CHO for example) : the calculated changeover from eclipsed to staggered conformations differentiates the semi-empirical methods from the empirical potential method used.     

The Structure of Cellulose by Conformational Analysis. 1. Cellobiose and Methyl-β-cellobioside

Conformational analysis studies on the tertiary structure of cellobiose and methyl-β-cellobioside were carried out by using calculations of van der Waals, H-bond, electrostatic, and torsional energy interactions between the atoms and groups of the molecules. Energy maps as functions of the rotational anglesΨo and Φ° of the glucosidic bond were obtained in increments of 20° and refined in increments of 1°. Two “primary” and one “secondary” conformations of minimum energy were obtained for both cellobiose and methyl-β-cellobioside, some of which are equivalent to results obtained by x-ray diffraction. The H-bond forces are shown to be, together with the van der Waals forces, the predominant factors in the fixation of the conformations of minimum energy. The position and energy contributions of the H-bonds patterns for the favored conformations are identified.     

Experimental and Theoretical Charge Density Study on Di‐2‐pyrazylamine (Hdpza) Molecule in Crystal

Electron density distribution of Di‐2‐pyrazylamine ( Hdpza ) is studied both by single‐crystal X‐ray diffraction method at 100K and theoretical calculation. Structural determination reveals that Hdpza molecules crystalize in a syn‐anti conformation with an intramolecular C? H?N hydrogen bond between two pyrazine rings and then gather together via two intermolecular N? H?N and C? H?N hydrogen interaction and π? π stacking interaction between pyrazine rings. Charge density analysis is made in terms of deformation density (Δπ), Laplacian distribution and topological analysis of total electron density based on multipole model and theoretical calculation. The agreement between experiment and theory is good. The topological properties at bond critical points of C? C and C? N bonds reveal a covalent bond character, and those of intermolecular interactions, such as hydrogen bonds and π? π stacking interactions, reveal a closed‐shell interaction. The potential energy curve of Hdpza molecule shows that the syn‐anti conformation is the most stable one (global minima) than the other two of syn‐syn and anti‐anti conformations.     

Nonbonded P···P and P···Se Interactions in Naphthalene 1,8-Positions: Role of Lone-Pair Orbitals

The lone pair-lone pair repulsion plays an important role in the nonbonded P;;;P interaction in naphthalene 1,8-positions. The conformations around P and Se in 8-(PhSe)-1-(Ph 2 P=O)C 10 H 6 are determined by the attractive O;;;Se--C 3c-4e type interaction. The P;;;Se interaction in the 1,8-positions is also discussed.     

Classification of polymer structures by graph theory

Compact polymers such as proteins obtain their unique conformation by appropriate nonbonded interactions among their monomer residues. Innumerable nonnative compact conformations are also possible, and it is essential to distinguish the native from the nonnative conformations. Toward this goal we have used graph‐theoretic methods to classify polymer structures formed by noncovalent interactions. All compact structures on a 4×4 two‐dimensional lattice and a few conformations on 3×3×3 cubic lattice have been investigated. The 69 compact conformations in 4×4 two‐dimensional lattice are classified into 12 groups based on the highest eigenvalue and eigenvector. The complex graphs obtained for polymers in a 3×3×3 lattice space are analyzed. Their eigenvalues and eigenvector components are correlated with the branching structure and the center of the graph. The method has application in classifying real polymers such as proteins into their substructures, cluster, and domains. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 71: 349–356, 1999