Density functional theory study of the interaction between formamide and uracil

The hydrogen bonding of complexes formed between the formamide and uracil molecule has been fully investigated in the present study using the density functional theory (DFT) method at varied basis set levels from 6‐31G to 6‐311++G(d,p). Eight stable cyclic structures with two hydrogen bonds involved in the interaction are found on the potential energy surface (PES). The four structures are seven‐membered rings; the others are eight‐membered rings. The eight‐membered ring is preferred over the seven‐membered one by analyzing the hydrogen bond lengths and the interaction energies. The infrared (IR) spectrum frequencies, IR intensities, and the vibrational frequency shifts are reported. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Cyclochiral resorcin[4]arenes as effective enantioselectors in the gas phase

The effect of cyclochirality of rccc‐2,8,14,20‐tetra‐n‐decyl‐4,10,16,22‐tetra‐O‐methylresorcin[4]arene (C) on the enantiodiscrimination of a number of chiral bidentate and tridentate aromatic and aliphatic biomolecules (G) has been investigated by nano‐electrospray ionization (nano‐ESI)‐Fourier transform ion cyclotron resonance mass spectrometry. The experimental approach is based on the formation of diastereomeric proton‐bound [C·H·G]⁺ complexes by nano‐ESI of solutions containing an equimolar amount of quasi‐enantiomers (C) together with the chiral guest (G) and the subsequent measurement of the rate of the G substitution by the attack of several achiral and chiral amines. In general, the heterochiral complexes react faster than the homochiral ones, except when G is an aminoalcoholic neurotransmitter whose complexes, beyond that, exhibit the highest enantioselectivity. The kinetic results were further supported by both collision‐induced dissociation experiments on some of the relevant [C₂·H·G]⁺ three‐body species and Density functional theory (DFT) calculations performed on the most selective systems. Copyright © 2012 John Wiley & Sons, Ltd.     

How can the Cross-Link Adducts Formed by Novel Trans Platinum Drug be Influenced by Hydrogen Bond

A systematic quantum chemical characterization of intrinsic structure, energies and spectral properties of all the studied cross-link adducts formed by the novel trans platinum with thiazole ligand has been carried out at B3LYP/6-31G^＊ level of theory with the Lanl2dz pseudo potential basis set for the Pt atom. Special attention has been paid to the relative stability of these complexes and the factors that probably alter the order of the relative stability. The important influence of hydrogen bond on the structures, the energies and the spectral property was revealed. Other factors that contribute to relative stability including solvation effect, entropy and electronic delocalization energy were taken into account. The stability energy of the whole complex, and the interaction energy between two purine bases and the [Pt-（NH3）thiazole]^2＋ group were adopted to study the interplay among subsystems and their contribution to relative stability of all the studied cross-link model. Finally, basic spectral properties of these complexes including H（8） chemical shifts of all the studied complexes and the VCD （vibrational circular dichroism） spectra of two pairs of GG chelate enantiomers, were provided in order to define the structure of the most possible duplex bearing novel trans platinum drug lesions.     

Theoretical study on the mechanism of the reaction for alkene hydroaminations catalyzed by chiral aldehyde

Alkene hydroamination catalyzed by chiral aldehyde relying only on temporary intramolecularity is a new concept reaction. In this article, the reaction mechanism was investigated using density functional theory. The calculation results show that: (1) The reaction can be divided into two parts. The first part is a dehydration process involving a hemiaminal formation. The nitrone catalyst forms through rapid intermolecular nucleophilic addition of benzylhydroxylamine to chiral aldehyde precatalyst. The second part is a catalytic cycle, which involves an aminal formation—hydroamination—ring opening—product release process. (2) There are four enantioselective pathways related to the products of S and R configurations. Enantioselectivity is attributed to the different forming ways of a planar five‐membered ring. The preferred pathways for the S‐configuration product ( S3 ) and R‐configuration product ( R3 ) are confirmed. © 2013 Wiley Periodicals, Inc.     

Density functional computations of alkynylation of ethanimine catalyzed by chiral zinc(II)‐complexes

The alkynylation of ethanimine catalyzed by chiral zinc(II)‐complexes was studied by means of the density functional theory (DFT). All the intermediates and transition states were optimized completely at the B3LYP/6‐31G(d,p) level. Calculation results confirm that the alkynylation of ethanimine is exothermic and the total released energy is about ?13 kJ/mol. The formation of the catalyst–alkynyl complexes M4 is the rate‐determining step for this alkynylation, and the formation of the catalyst–amine complexes M5 is the chirality‐limiting step for this alkynylation. The transition states for the chirality‐limiting step have a H? O? Zn? C? C? N six‐membered ring. The dominant products predicted theoretically for this alkynylation are, respectively, S‐amine for ethanimine anti and R‐amine for ethanimine syn . © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Natural terpene derivatives as new structural task‐specific ionic liquids to enhance the enantiorecognition of acidic enantiomers on teicoplanin‐based stationary phase by high‐performance liquid chromatography

We present the specific cooperative effect of a semisynthetic glycopeptide antibiotic teicoplanin and chiral ionic liquids containing the (1R ,2S ,5R )‐(–)‐menthol moiety on the chiral recognition of enantiomers of mandelic acid, vanilmandelic acid, and phenyllactic acid. Experiments were performed chromatographically on an Astec Chirobiotic T chiral stationary phase applying the mobile phase with the addition of the chiral ionic liquids. The stereoselective binding of enantiomers to teicoplanin in presence of new chiral ionic liquids were evaluated applying thermodynamic measurements and the docking simulations. Both the experimental and theoretical methods revealed that the chiral recognition of enantiomers in the presence of new chiral ionic liquids was enthalpy driven. The changes of the teicoplanin conformation occurring upon binding of the chiral ionic liquids are responsible for the differences in the standard changes in Gibbs energy (ΔG ⁰) values obtained for complexes formed by the R and S enantiomers and teicoplanin. Docking simulations revealed the steric adjustment between the chiral ionic liquids cyclohexane ring (chair conformation) and the β‐d ‐glucosamine ring of teicoplanin and additionally hydrophobic interactions between the decanoic aliphatic chain of teicoplanin and the alkyl group of the tested salts. The obtained terpene derivatives can be considered as “structural task‐specific ionic liquids” responsible for enhancing the chiral resolution in synergistic systems with two chiral selectors.     

Rearrangements in Model Peptide‐Type Radicals via Intramolecular Hydrogen‐Atom Transfer

Intramolecular H‐atom transfer in model peptide‐type radicals was investigated with high‐level quantum‐chemistry calculations. Examination of 1,2‐, 1,3‐, 1,5‐, and 1,6[C ? N]‐H shifts, 1,4‐ and 1,7[C ? C]‐H shifts, and 1,4[N ? N]‐H shifts (Scheme 1), was carried out with a number of theoretical methods. In the first place, the performance of UB3‐LYP (with the 6‐31G(d), 6‐31G(2df,p), and 6‐311+G(d,p) basis sets) and UMP2 (with the 6‐31G(d) basis set) was assessed for the determination of radical geometries. We found that there is only a small basis‐set dependence for the UB3‐LYP structures, and geometries optimized with UB3‐LYP/6‐31G(d) are generally sufficient for use in conjunction with high‐level composite methods in the determination of improved H‐transfer thermochemistry. Methods assessed in this regard include the high‐level composite methods, G3(MP2)‐RAD, CBS‐QB3, and G3//B3‐LYP, as well as the density‐functional methods B3‐LYP, MPWB1K, and BMK in association with the 6‐31+G(d,p) and 6‐311++G(3df,3pd) basis sets. The high‐level methods give results that are close to one another, while the recently developed functionals MPWB1K and BMK provide cost‐effective alternatives. For the systems considered, the transformation of an N‐centered radical to a C‐centered radical is always exothermic (by 25 kJ ? mol^?1 or more), and this can lead to quite modest barrier heights of less than 60 kJ ? mol^?1 (specifically for 1,5[C ? N]‐H and 1,6[C ? N]‐H shifts). H‐Migration barriers appear to decrease as the ring size in the transition structure (TS) increases, with a lowering of the barrier being found, for example when moving from a rearrangement proceeding via a four‐membered‐ring TS (e.g., the 1,3[C ? N]‐H shift, CH₃? C(O)? NH^. → ^.CH₂? C(O)? NH₂) to a rearrangement proceeding via a six‐membered‐ring TS (e.g., the 1,5[C ? N]‐H shift, ^.NH? CH₂? C(O)? NH? CH₃ → NH₂? CH₂? C(O)? NH? CH₂^.).     

Synthesis,Structural Characterisation and Stereochemical Investigation of Chiral Sulfur‐Functionalised N‐Heterocyclic Carbene Complexes of Palladium and Platinum

Palladium and platinum complexes containing a sulfur‐functionalised N‐heterocyclic carbene (S‐NHC) chelate ligand have been synthesised. The absolute conformations of these novel organometallic S‐NHC chelates were determined by X‐ray structural analyses and solution‐phase 2D ¹H–¹H ROESY NMR spectroscopy. The structural studies revealed that the phenyl substituents on the stereogenic carbon atoms invariably take up the axial positions on the Pd‐C‐S coordination plane to afford a skewed five‐membered ring structure. All of the chiral complexes are structurally rigid and stereochemically locked in a chiral ring conformation that is either (R_s,S,R)‐λ or (S_s,R,R)‐δ in both the solid state and solution.     

Enantiomer resolution of intrinsically chiral C21-alkylated N-confused porphyrin complexes

The resolution of stereoisomers of C21‐alkylated nickel(II) complexes of N‐confused porphyrin (NCP) was performed by means of chiral‐phase HPLC with an effectiveness of above 90 % molar ratio for each isomer. The reverse signs of the Cotton effects in the circular dichroism (CD) spectra of the separated fractions are indicative of the pair of enantiomers. The application of low‐temperature 2D NMR methods to the separated diastereomers of the system comprising a chiral 2‐(S)‐methylbutyl substituent, in connection with the CD spectra and relative HPLC migration rates, allowed the assignment of the absolute configuration of the chiral C21‐substituted complexes of NCP. The assignment was confirmed by time‐dependent DFT (TDDFT) calculations of CD spectra for the C21‐methylated nickel(II) complex. The system remains chiral after removal of the metal ion from the macrocyclic crevice, despite the fact that this demetalation is connected with a change of the C21 hybridization from pyramidal to trigonal. The retention of chirality was established by means of CD spectra and confirmed by TDDFT calculations for a C21‐methylated NCP free base. Stereoisomers were also separated for three covalently linked bis(NCP) systems with bridges involving one or two C21 carbon atoms. The occurrence of a pair of enantiomers was established for nonsymmetrical dimers comprising only one stereogenic center. In the case of the 21,21′‐(o‐xylene)‐linked dimer, three stereoisomers, that is, a pair of enantiomers and an optically inactive meso‐form, were separated and analyzed by CD and ¹H NMR spectroscopy. The stereoisomers of a diastereoselectively formed nonsymmetrical chloroplatinum(II)‐linked dimer, consisting of heterochiral C21‐alkylated NCP nickel(II) subunits, after separation displayed a strong optical activity, which can be ascribed to the rigid helical structure of the complex.     

Distinguishing Enantiomers by Tip‐Enhanced Raman Scattering: Chemically Modified Silver Tip with an Asymmetric Atomic Arrangement

Discrimination between enantiomers is achieved by tip‐enhanced Raman scattering (TERS) using a silver tip that is chemically modified by an achiral para‐mercaptopyridine (pMPY) probe molecule. Differences in the relative intensities of the pMPY spectra were monitored for three pairs of enantiomers containing hydroxy (?OH) and/or amino (?NH₂) groups. The N: or N⁺?H functionality of the pMPY‐modified tip participates in hydrogen‐bond interactions with a particular molecular orientation of each chiral isomer. The asymmetric arrangement of silver atoms at the apex of the tip induces an asymmetric electric field, which causes the tip to become a chiral center. Differences in the charge‐transfer (CT) states of the metal‐achiral probe system in conjunction with the asymmetric electric field produce different enhancements in the Raman signals of the two enantiomers. The near‐field effect of the asymmetric electric field, which depends on the number of analyte functional groups capable of hydrogen‐bond formation, improves the degree of discrimination.     

An improved molecular modeling method for the prediction of enantioselectivity

An improved method for the calculation of enantioselectivity by molecular mechanics is presented. This method does not use any a priori assumption on the conformation of the molecules in the complex and is equally applicable to weak as well as very strong complexes. High-temperature molecular dynamics is used for the creation of a large number (5000–20,000) of random conformations and configurations of a 1:1 (or 1:2) complex of chiral molecules with a chiral selector. All configurations are energy minimized. The data set is only accepted if all lowest-energy complexes occur at least five times in the minimized data set. The enantioselectivity is then calculated from the free energies of the diasteromeric complexes (chiral chromatography) or from the ratio of the sum of the Boltzmann weights (distribution of enantiomers over a chiral organic phase and a nonchiral water phase). This approach has been successfully applied to a range of chiral compounds. These include a weakly bonded Pirkle chiral stationary phase (CSP) system, a strong complex of diprotonated 1,2-diphenyl-1,2-diamino-ethane with two molecules of R,R-tartrate, and the intermediate-strength complexes of protonated and of neutral norephedrine with R,R-tartrate. © 1995 by John Wiley & Sons, Inc.     

Asymmetric Substitutions of 2‐Lithiated N‐Boc‐piperidine and N‐Boc‐azepine by Dynamic Resolution

Proton abstraction of N‐tert‐butoxycarbonyl‐piperidine (N‐Boc‐piperidine) with sBuLi and TMEDA provides a racemic organolithium that can be resolved using a chiral ligand. The enantiomeric organolithiums can interconvert so that a dynamic resolution occurs. Two mechanisms for promoting enantioselectivity in the products are possible. Slow addition of an electrophile such as trimethylsilyl chloride allows dynamic resolution under kinetic control (DKR). This process occurs with high enantioselectivity and is successful by catalysis with substoichiometric chiral ligand (catalytic dynamic kinetic resolution). Alternatively, the two enantiomers of this organolithium can be resolved under thermodynamic control with good enantioselectivity (dynamic thermodynamic resolution, DTR). The best ligands found are based on chiral diamino‐alkoxides. Using DTR, a variety of electrophiles can be used to provide an asymmetric synthesis of enantiomerically enriched 2‐substituted piperidines, including (after Boc deprotection) the alkaloid (+)‐β‐conhydrine. The chemistry was extended, albeit with lower yields, to the corresponding 2‐substituted seven‐membered azepine ring derivatives.     

Geometry and Conformation of Thietanium Ions from Diffraction Data and Ab Initio Calculations

Four‐membered ring thiosulfonium ions may be obtained quantitatively and under mild conditions by anionotropic rearrangement of C‐(tert‐butyl)‐substituted thiiranium ion precursors. Thus, t‐4‐(tert‐butyl)‐r‐1,2,2,c‐3‐tetramethylthietanium tetrafluoroborate or hexachloroantimonate ( 2a or 2b , resp.) were formed from thiiranium ion 1 . The thietanium salts 2a and 2b were characterized by X‐ray crystal‐structure analysis. Their cation geometry was also optimized by ab initio calculations at the RHF/6‐31G*//RHF/6‐31G* level, as were those of its stereoisomer 3 and of the unsubstituted S‐methylthietanium ion 5 . Comparison of 2 , 3 , and 5 with 4 – the only other thietanium ion studied by XRD, where the C‐atoms of the thioniacyclobutane ring are part of a trinorbornane skeleton – indicates that, in these systems, relief from substituent overcrowding is easily achieved by a folding of the four‐membered ring along the line connecting the two opposite C‐atoms. The corresponding ring‐deformation normal mode has a calculated frequency as low as 109 cm⁻¹ in ion 5 , to be compared with a frequency of 138 cm⁻¹ in methylcyclobutane. For thietanium ion 2 , the frequencies of the two normal modes involving such ring deformation have calculated values of 61 and 85 cm⁻¹.     

Theoretical studies on the structures and isomerization of methylene lithium‐chlorosilylenoid H2CSiLiCl

The methylene lithium‐chlorosilylenoid H₂C?SiLiCl was studied with ab initio calculations at the G2(MP2) level. Its four equilibrium structures, p‐complex, three‐membered ring, σ complex and silene, and three isomerization transition states were located. The calculations show that the nonplanar p‐complex structure is the lowest in energy among four equilibrium structures of H₂C?SiLiCl and should be experimentally detectable. The silene and σ complex structures with high energies are unstable and easy to isomerize to the most stable p‐complex structure via three‐membered ring one. Also, the geometric characteristics and bonding properties of various structures were analyzed and discussed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Fluorine as a Regiocontrol Element in the Ring Opening of Bicyclic Aziridiniums

The origin of the variation in the regioselectivity of the nucleophilic ring opening of a series of bicyclic aziridinium ions derived from N‐alkylprolinols was investigated by quantum‐chemical computations (M06‐2X/6‐31+G(d,p)‐SMD). These aziridiniums differ only in the degree and the configurations of F‐substitution at C(4). With the azide ion as nucleophile, the ratio of the piperidine to the pyrrolidine product was computed. An electrostatic gauche effect influences the conformation of the adjoining five‐membered ring in the fluorinated bicyclic aziridinium. This controls the regioselectivity of the aziridinium ring opening.     

量子化学计算解析手性共价有机框架材料6色谱固定相的手性拆分机理

为探究手性共价有机框架材料6(Chiral Covalent Organic Frameworks 6, CCOF6)色谱固定相的手性拆分机理,首先运用ORCA程序对CCOF6及4对手性对映体进行结构优化,然后使用AutoDock程序对CCOF6及各对映体分子进行分子对接,获得CCOF6与对映体相互作用的初始构型;采用ORCA程序(B3LYP泛函,带DFT-D3校正,轨道基组为def2-TZVP, def2/J作为RI-J的辅助基组,RIJCOSX用来加速计算)对初始构型进行能量计算,以最终确定CCOF6与对映体的相互作用构型,并获得相应的结合自由能和结合自由能差;使用Multiwfn程序对ORCA结果进行独立梯度模型分析,并应用视觉分子动力学程序可视化展示CCOF6与对映体的弱相互作用。结果表明:①在计算结合自由能方面,考虑了溶剂效应的ORCA计算方法比不考虑溶剂效应的ORCA以及AutoDock计算方法更为精确;②CCOF6色谱固定相与对映体之间的结合自由能差绝对值越大,对映体的选择性因子也越大,然而对映体的分离度不一定会越大;③除S-1-苯基-1-丙醇是以羟基和CCOF6的醚键发生相互作用外,其他对映体皆为羟基与CCOF6的羰基发生相互作用,且S-1-苯基-1-丙醇与CCOF6的结合力最弱;④结合对映体的出峰时间和其与CCOF6的结合自由能大小可以推断,正己烷/异丙醇流动相对1-苯基-1-丙醇的洗脱能力最弱,正己烷/异丙醇流动相对1-苯基-2-丙醇的洗脱能力次弱;⑤除了S-1-苯基-1-丙醇出峰时间迟于R-1-苯基-1-丙醇,其余对映体均为R型出峰时间迟于S型。     

Isomerization study of C5H5NO molecules

The complex potential energy surface (PES) for the isomerization of C₅H₅NO species, including 18 isomers and 23 interconversion transition states, is probed theoretically at the B3LYP/6‐311++G(d,p) and MP2//B3LYP/6‐311++G(d,p) levels of theory. The geometries and relative energies for various stationary points were determined. The zero‐point vibrational energy (ZPVE) corrections have been made to calculate the reliable energy. We predicted a six‐membered ring structure as a global minima isomer I, which is 118.49 and 131.48 kcal · mol^?1 more stable than the least stable, four‐ and three‐membered ring isomer VIII at B3LYP and MP2//B3LYP levels of theory, respectively. The isomers and interconversion transition states have verified by frequency calculation. The intrinsic reaction coordinates (IRC) calculations have been performed to confirm that each transition state is linked by the desired reactants and products. The isomer stability has been studied using relative energies, chemical hardness, and chemical potential. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Ab initio Study of Mechanism of Cycloaddition Reaction between Germylene Silylene (H2GeSi:) and Acetone

The mechanism of the cycloaddition reaction between singlet germylene silylene (H₂GeSi:) and acetone has been investigated with CCSD(T)/6‐31G*//MP2/6‐31G* method. From the potential energy profile, we could predict that the reaction has two competitive dominant reaction channels. The present rule of this reaction is that the [2+2] cycloaddition reaction of the two (‐bonds in germylene silylene and acetone generates a four‐membered ring silylene with Ge. Because of the unsaturated property of Si atom in the four‐membered ring silylene with Ge, it could further react with acetone, resulting in the generation of a bis‐heterocyclic compound with Si and Ge. Simultaneously, the ring strain of the four‐membered ring silylene with Ge makes it isomerize to a twisted four‐membered ring product.     

Quantum chemical study on enantioselective reduction of keto oxime ether with borane catalyzed by oxazaborolidine. Part 2. Structures of catalyst‐alkoxyborane adduct with a four‐membered ring and succeeding reaction intermediates

Quantum chemical ab initio computations of the structures and properties of oxazaborolidine‐alkoxyborane adduct with a B? N? B? O four‐membered ring and succeeding reaction intermediates are carried out in the current work by means of the Hartree–Fock (HF) and the density functional methods. All the structures are optimized completely at the HF/6‐31G(d) and Becke's three‐parameter exchange functional and the gradient‐corrected functional of Lee, Yang, and Paar (B3LYP)/6‐31G(d) levels. As shown in the obtained results, the oxazaborolidine‐alkoxyborane adduct with a B? N? B? O four‐membered ring may be formed during the reduction of the carbonyl bond of the catalyst‐borane‐keto oxime ether adduct. The breakdown of the B? N? B? O four‐membered ring results in the formation of the adduct with a B? N? B? O? C? C? N seven‐membered ring and an oxime bond. The reduction of the oxime bond leads to the adduct with a chiral oxime carbon. The B(2)? N_{C? N} bond in the B? N? B? O? C? C? N seven‐membered ring of the adduct with a reduced oxime bond is weaker comparatively and thus may be more easily broken down. All the adducts have four stable structures. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 93: 294–306, 2003     

Phosphoryl group differentiating α‐amino acids from β‐ and γ‐amino acids in prebiotic peptide formation

In recent years β‐amino acids have increased their importance enormously in defining secondary structures of β‐peptides. Interest in β‐amino acids raises the question: Why and how did nature choose α‐amino acids for the central role in life? In this article we present experimental results of MS and ³¹P NMR methods on the chemical behavior of N‐phosphorylated α‐alanine, β‐alanine, and γ‐amino butyric acid in different solvents. N‐Phosphoryl α‐alanine can self‐assemble to N‐phosphopeptides either in water or in organic solvents, while no assembly was observed for β‐ or γ‐amino acids. An intramolecular carboxylic–phosphoric mixed anhydride (IMCPA) is the key structure responsible for their chemical behaviors. Relative energies and solvent effects of three isomers of IMCPA derived from α‐alanine (2a–c), with five‐membered ring, and five isomers of IMCPA derived from β‐alanine (4a–e), with six‐membered ring, were calculated with density functional theory at the B3LYP/6‐31G** level. The lower relative energy (3.2 kcal/mol in water) of 2b and lower energy barrier for its formation (16.7 kcal/mol in water) are responsible for the peptide formation from N‐phosphoryl α‐alanine. Both experimental and theoretical studies indicate that the structural difference among α‐, β‐, and γ‐amino acids can be recognized by formation of IMCPA after N‐phosphorylation. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 232–241, 2003