Ab Initio Study on the Potential Energy Surfaces of B4 Cluster

The singlet and triplet potential energy surfaces (PES) for the isomerization and dissociation reactions of B₄ isomers have been investigated using ab initio methods. Ten B4 isomers have been identified and of these 10 species, 4 have not been reported previously. The singlet rhombic structure ¹1 is found to be the most stable on the B₄ surface, in agreement with the results of previous reports. Several isomerization and dissociation pathways have been found. On the singlet PES, the linear ¹3b can rearrange to rhombus ¹1 directly, while ¹3c rearranges to ¹1 through two‐step reactions involving a cyclic intermediate. On the triplet PES, the capped triangle structure ³2 undergoes ring opening to the linear isomer ³3b with a barrier of 34.8 kcal/mol and 44.9 kcal/mol, and the latter undergoes ring closure to the square structure ³1 with a barrier of 30.4 kcal/mol and 33.0 kcal/mol at the MP4/6–311+G(3df)//MP2/6–311G(d) and CCSD/aug‐cc‐pVTZ//MP2/6–311G(d) levels of theory, respectively. The direct decomposition of singlet B₄ yielding to B₃+B is shown to have a large endothermicity of 87.3 kcal/mol (CCSD), and that producing 2B₂ to have activation energy of 133.4 kcal/mol (CCSD).     

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     

Highly Stereoselective β‐Mannopyranosylation via the 1‐α‐Glycosyloxy‐isochromenylium‐4‐gold(I) Intermediates

While the gold(I)‐catalyzed glycosylation reaction with 4,6‐O‐benzylidene tethered mannosyl ortho‐alkynylbenzoates as donors falls squarely into the category of the Crich‐type β‐selective mannosylation when Ph₃PAuOTf is used as the catalyst, in that the mannosyl α‐triflates are invoked, replacement of the ^?OTf in the gold(I) complex with less nucleophilic counter anions (i.e., ^?NTf₂, ^?SbF₆, ^?BF₄, and ^?BAr₄^F) leads to complete loss of β‐selectivity with the mannosyl ortho‐alkynylbenzoate β‐donors. Nevertheless, with the α‐donors, the mannosylation reactions under the catalysis of Ph₃PAuBAr₄^F (BAr₄^F=tetrakis[3,5‐bis(trifluoromethyl)phenyl]borate) are especially highly β‐selective and accommodate a broad scope of substrates; these include glycosylation with mannosyl donors installed with a bulky TBS group at O3, donors bearing 4,6‐di‐O‐benzoyl groups, and acceptors known as sterically unmatched or hindered. For the ortho‐alkynylbenzoate β‐donors, an anomerization and glycosylation sequence can also ensure the highly β‐selective mannosylation. The 1‐α‐mannosyloxy‐isochromenylium‐4‐gold(I) complex ( Cα ), readily generated upon activation of the α‐mannosyl ortho‐alkynylbenzoate ( 1 α ) with Ph₃PAuBAr₄^F at ?35 °C, was well characterized by NMR spectroscopy; the occurrence of this species accounts for the high β‐selectivity in the present mannosylation.     

Embedding of the saddle point of index two on the PES of the ring opening of cyclobutene

The ring opening of cyclobutene is characterized by a competition of the two different pathways: a usual pathway over a saddle of index one (SP₁) along the conrotatory behavior of the end groups, as well as a “forbidden” pathway over a saddle point of index two (SP₂) along the disrotatory behavior of the end CH₂ groups. We use the system of ordinary differential equations for the method of the gentlest ascent dynamics (GAD) to determine saddle points of the potential energy surface (PES) of the ring opening of cyclobutene to cis‐butadiene. We apply generalized GAD formulas for the search of a saddle point of index two. To understand the relation of the different regions of the PES (around minimums, around SPs of index one or two) we also calculate valley‐ridge inflection (VRI) points on the PES using Newton trajectories (NT). VRIs and the corresponding singular NTs subdivide the regions of “attraction” of the different SPs. We calculate the connections of the SP₂ (in its different symmetry versions) with different SPs of index one of the PES by different “reaction pathways.” We compare the possibilities of the tool of the GAD curves for the exploration of PESs with these of NT. The barrier of the disrotatory SP₂ is somewhat higher than the barrier of the conrotatory SP₁, however, pathways across the slope to the SP₂ open additional reaction valleys. © 2015 Wiley Periodicals, Inc.     

2,3,4,6‐Tetra‐O‐acetyl‐α‐d‐glucopyranosyl azide

The Cu^I‐catalysed 1,3‐dipolar cycloaddition of an azide and a terminal alkyne is becoming an increasingly popular tool for synthetic chemists. This is the most representative of the so‐called `click reactions' and it is used to generate 1,4‐disubstituted triazoles in high yield. During studies on such cycloaddition reactions, a reduced reactivity of an α‐glucosyl azide with respect to the corresponding β‐anomer was observed. With the aim of understanding this phenomenon, the structure of the title compound, C₁₄H₁₉N₃O₉, has been determined at 140 K. The glucopyranosyl ring appears in a regular ⁴C₁ chair conformation with all the substituents in equatorial positions, except for the anomeric azide group, which adopts an axial orientation. The observed bond lengths are consistent with a strong anomeric effect, which is reflected in a change in dipolar character and hence reduced reactivity of the α‐glucosyl azide.     

Quantum chemical exploration of formaldehyde clusters (H2CO)n (n = 2–4)

Global exploration of equilibrium structures and interconversion pathways on the quantum chemical potential energy surface (PES) is performed for (H₂CO)n (n = 2–4) by using the Scaled Hypersphere Search‐Anharmonic Downward Distortion Following (SHS‐ADDF) method. Density functional theoretical (DFT) calculations with empirical dispersion corrections (D3) yielded comparable results for formaldehyde dimer in comparison with recent detailed studies at CCSD(T) levels. Based on DFT‐D3 calculations, trimer and tetramer structures and their stabilities were studied. For tetramer, a highly symmetrical S₄ structure was found as the most stable form in good accordance with experimentally determined tetramer unit in the formaldehyde crystal. © 2018 Wiley Periodicals, Inc.     

Ab initio study on the reaction mechanism of ozone with bromine atom

Ab initio calculations of the potential energy surface (PES) for the Br+O₃ reaction have been performed using the MP2, CCSD(T), and QCISD(T) methods with 6‐31G(d), 6‐311G(d), and 6‐311+G(3df). The reaction begins with a transition state (TS) when the Br atom attacks a terminal oxygen of ozone, producing an intermediate, the bromine trioxide (M), which immediately dissociates to BrO+O₂. The geometry optimizations of the reactants, products, and intermediate and transition states are carried out at the MP2/6‐31G(d) level. The reaction potential barrier is 3.09 kcal/mol at the CCSD(T)/6‐311+G(3df)//MP2 level, which shows that the bromine atom trends intensively to react with the ozone. The comparison of the Br+O₃ reaction with the F+O₃ and Cl+O₃ reactions indicates that the reactions of ozone with the halogen atoms have the similar reaction mechanism. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

12‐ to 22‐Membered Bridged β‐Lactams as Potential Penicillin‐Binding Protein Inhibitors

As potential inhibitors of penicillin‐binding proteins (PBPs), we focused our research on the synthesis of non‐traditional 1,3‐bridged β‐lactams embedded into macrocycles. We synthesized 12‐ to 22‐membered bicyclic β‐lactams by the ring‐closing metathesis (RCM) of bis‐ω‐alkenyl‐3(S)‐aminoazetidinone precursors. The reactivity of 1,3‐bridged β‐lactams was estimated by the determination of the energy barrier of a concerted nucleophilic attack and lactam ring‐opening process by using ab initio calculations. The results predicted that 16‐membered cycles should be more reactive. Biochemical evaluations against R39 DD‐peptidase and two resistant PBPs, namely, PBP2a and PBP5, revealed the inhibition effect of compound 4d , which featured a 16‐membered bridge and the N‐tert‐butyloxycarbonyl chain at the C3 position of the β‐lactam ring. Surprisingly, the corresponding bicycle, 12d , with the PhOCH₂CO side chain at C3 was inactive. Reaction models of the R39 active site gave a new insight into the geometric requirements of the conformation of potential ligands and their steric hindrance; this could help in the design of new compounds.     

Theoretical studies of mechanisms of cycloaddition reaction between difluoromethylene carbene and acetone

Mechanisms of the cycloaddition reaction between singlet difluoromethylene carbene and acetone have been investigated with the second‐order Møller–Plesset (MP2)/6‐31G* method, including geometry optimization and vibrational analysis. Energies for the involved stationary points on the potential energy surface (PES) are corrected by zero‐point energy (ZPE) and CCSD(T)/6‐31G* single‐point calculations. From the PES obtained with the CCSD(T)//MP2/6‐31G* method for the cycloaddition reaction between singlet difluoromethylene carbene and acetone, it can be predicted that path B of reactions 2 and 3 should be two competitive leading channels of the cycloaddition reaction between difluoromethylene carbene and acetone. The former consists of two steps: (i) the two reactants first form a four‐membered ring intermediate, INT2, which is a barrier‐free exothermic reaction of 97.8 kJ/mol; (ii) the intermediate INT2 isomerizes to a four‐membered product P_2b via a transition state TS2b with an energy barrier of 24.9 kJ/mol, which results from the methyl group transfer. The latter proceeds in three steps: (i) the two reactants first form an intermediate, INT1c, through a barrier‐free exothermic reaction of 199.4 kJ/mol; (ii) the intermediate INT1c further reacts with acetone to form a polycyclic intermediate, INT3, which is also a barrier‐free exothermic reaction of 27.4 kJ/mol; and (iii) INT3 isomerizes to a polycyclic product P₃ via a transition state TS3 with an energy barrier of 25.8 kJ/mol. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

α‐Halogenoacetanilides as Hydrogen‐Bonding Organocatalysts that Activate Carbonyl Bonds: Fluorine versus Chlorine and Bromine

α‐Halogenoacetanilides (X=F, Cl, Br) were examined as H‐bonding organocatalysts designed for the double activation of C?O bonds through NH and CH donor groups. Depending on the halide substituents, the double H‐bond involved a nonconventional C?H???O interaction with either a H?CX_n (n=1–2, X=Cl, Br) or a H?C_Ar bond (X=F), as shown in the solid‐state crystal structures and by molecular modeling. In addition, the catalytic properties of α‐halogenoacetanilides were evaluated in the ring‐opening polymerization of lactide, in the presence of a tertiary amine as cocatalyst. The α‐dichloro‐ and α‐dibromoacetanilides containing electron‐deficient aromatic groups afforded the most attractive double H‐bonding properties towards C?O bonds, with a N?H???O???H?CX₂ interaction.     

Direct Ab Initio Dynamics Study on the Reaction of CH3CHF2 (HFC‐152a) with the Cl Atom

A direct ab initio dynamics method is used to investigate the hydrogen‐abstraction reaction CH₃CHF₂+Cl. One transition state is located for α‐H abstraction, and two are identified for β‐H abstraction. The potential‐energy surface (PES) is obtained at the G3(MP2)//MP2/6‐311G(d, p) level. Furthermore, the rate constants of the three channels are evaluated by using canonical variational transition‐state theory (CVT) with small‐curvature tunneling (SCT) contributions over a wide temperature range of 200–2500 K. The dynamic calculations show that the reaction proceeds mainly by α‐H abstraction over the whole temperature range. The calculated rate constants and branching ratios are both in good agreement with the available experimental values.     

Quantum mechanical studies on model α‐pleated sheets

Pauling and Corey proposed a pleated‐sheet configuration, now called α‐sheet, as one of the protein secondary structures in addition to α‐helix and β‐sheet. Recently, it has been suggested that α‐sheet is a common feature of amyloidogenic intermediates. We have investigated the stability of antiparallel β‐sheet and two conformations of α‐sheet in solution phase using the density functional theoretical method. The peptides are modeled as two‐strand acetyl‐(Ala)₂‐N‐methylamine. Using stages of geometry optimization and single point energy calculation at B3LYP/cc‐pVTZ//B3LYP/6‐31G* level and including zero‐point energies, thermal, and entropic contribution, we have found that β‐sheet is the most stable conformation, while the α‐sheet proposed by Pauling and Corey has 13.6 kcal/mol higher free energy than the β‐sheet. The α‐sheet that resembles the structure observed in molecular dynamics simulations of amyloidogenic proteins at low pH becomes distorted after stages of geometry optimization in solution. Whether the α‐sheets with longer chains would be increasingly favorable in water relative to the increase in internal energy of the chain needs further investigation. Different from the quantum mechanics results, AMBER parm94 force field gives small difference in solution phase energy between α‐sheet and β‐sheet. The predicted amide I IR spectra of α‐sheet shows the main band at higher frequency than β‐sheet. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Probing the reactivity of microhydrated α‐nucleophile in the anionic gas‐phase SN2 reaction

To probe the kinetic performance of microsolvated α‐nucleophile, the G2(+)_M calculations were carried out for the gas‐phase S_N2 reactions of monohydrated and dihydrated α‐oxy‐nucleophiles XO^?(H₂O)_{n = 1,2} (X = HO, CH₃O, F, Cl, Br), and α‐sulfur‐nucleophile, HSS^?(H₂O)_{n = 1,2}, toward CH₃Cl. We compared the reactivities of hydrated α‐nucleophiles to those of hydrated normal nucleophiles. Our calculations show that the α‐effect of monohydrated and dihydrated α‐oxy‐nucleophiles will become weaker than those of unhydrated ones if we apply a plot of activation barrier as a function of anion basicity. Whereas the enhanced reactivity of monohydrated and dihydrated ROO^? (R = H, Me) could be observed if compared them with the specific normal nucleophiles, RO^? (R = H, Me). This phenomena can not be seen in the comparisons of XO^?(H₂O)_{n = 1,2} (X = F, Cl, Br) with ClC₂H₄O^?(H₂O)_{n = 1,2}, a normal nucleophile with similar gas basicity to XO^?(H₂O)_{n = 1,2}. These results have been carefully analyzed by natural bond orbital theory and activation strain model. Meanwhile, the relationships between activation barriers with reaction energies and the ionization energies of α‐nucleophile are also discussed. © 2015 Wiley Periodicals, Inc.     

Heteroatom‐Guided Torquoselective Olefination of α‐Oxy and α‐Amino Ketones via Ynolates

Ynolates were found to react with α‐alkoxy‐, α‐siloxy‐, and α‐aryloxyketones at room temperature to afford tetrasubstituted olefins with high Z selectivity. Since the geometrical selectivity was determined in the ring opening of the β‐lactone enolate intermediates, the torquoselectivity was controlled by the ethereal oxygen atoms. From experimental and theoretical studies, the high Z selectivity is induced by orbital and steric interactions rather than by chelation. In a similar manner, α‐dialkylamino ketones provided olefins with excellent Z selectivity. These products can be easily converted into multisubstituted butenolides and γ‐butyrolactams in good yield.     

Achieving High‐Temperature Stability of Metastable α‐MoC1‐x by Suppressing Phase Transformation with Mounted Atoms for Lithium Storage Performance

Despite a significant advancement in preparing metastable materials, one common problem is the strict and precious reaction conditions due to their metastable structures. Herein, we achieved the preparation of high‐temperature stabilized metastable α‐MoC_1?x by mounting zinc atoms into its lattice structure. Such a structural construction could suppress the phase transformation from α‐MoC_1?x to β‐Mo₂C through restricting the displacement of Mo atoms upon increased temperature. The resultant metastable α‐MoC_1?x can be stabilized up to 1000 °C and this stability temperature is the highest for the metastable α‐MoC_1?x so far. Synchrotron X‐ray absorption spectroscopy (XAS) and X‐ray photoelectron spectroscopy (XPS) confirm the structure of Zn‐mounted α‐MoC_1?x. Density functional theory (DFT) calculations reveal that the introduction of the Zn atoms in the lattice structure of α‐MoC_1?x could significantly decrease the energy difference (ΔE) between α‐MoC_1?x and β‐Mo₂C, thus effectively suppressing the phase transformation from α‐MoC_1?x to β‐Mo₂C and accordingly maintaining the high‐temperature stability of α‐MoC_1?x. This novel strategy can be used as a universal method to be extended to synthesize metastable α‐MoC_1?x from different precursors or other mounted elements. Moreover, the optimal product exhibits excellent lithium storage performances in terms of the cycling stability and rate performance.     

Enantioselective NHC‐Catalyzed Redox [2+2] Cycloadditions with Perfluoroketones: A Route to Fluorinated Oxetanes

The N‐heterocyclic carbene (NHC) catalyzed redox formal [2+2] cycloaddition between α‐aroyloxyaldehydes and perfluoroketones, followed by ring‐opening in situ delivers a variety of perfluorinated β‐hydroxycarbonyl compounds in good yield, and excellent diastereo‐ and enantioselectivity. Through a reductive work‐up and subsequent cyclization, this protocol offers access to highly substituted fluorinated oxetanes in two steps and in high ee.     

Nearly Degenerate Isomers of C(BH)2: Cumulene,Carbene, or Carbone?

The ground electronic state of C(BH)₂ exhibits both a linear minimum and a peculiar angle‐deformation isomer with a central B‐C‐B angle near 90°. Definitive computations on these species and the intervening transition state have been executed by means of coupled‐cluster theory including single and double excitations (CCSD), perturbative triples (CCSD(T)), and full triples with perturbative quadruples (CCSDT(Q)), in concert with series of correlation‐consistent basis sets (cc‐pVXZ, X=D, T, Q, 5, 6; cc‐pCVXZ, X=T, Q). Final energies were pinpointed by focal‐point analyses (FPA) targeting the complete basis‐set limit of CCSDT(Q) theory with auxiliary core correlation, relativistic, and non‐Born–Oppenheimer corrections. Isomerization of the linear species to the bent form has a minuscule FPA reaction energy of 0.02 kcal mol^?1 and a corresponding barrier of only 1.89 kcal mol^?1. Quantum tunneling computations reveal interconversion of the two isomers on a timescale much less than 1 s even at 0 K. Highly accurate CCSD(T)/cc‐pVTZ and composite c～CCSDT(Q)/cc‐pCVQZ anharmonic vibrational frequencies confirm matrix‐isolation infrared bands previously assigned to linear C(BH)₂ and provide excellent predictions for the heretofore unobserved bent isomer. Chemical bonding in the C(BH)₂ species was exhaustively investigated by the atoms‐in‐molecules (AIM) approach, molecular orbital plots, various population analyses, local mode vibrations and force constants, unified reaction valley analysis (URVA), and other methods. Linear C(BH)₂ is a cumulene, whereas bent C(BH)₂ is best characterized as a carbene with little carbone character. Weak B–B attraction is clearly present in the unusual bent isomer, but its strength is insufficient to form a CB₂ ring with a genuine boron–boron bond and attendant AIM bond path.     

Poly(bis‐2,2,2‐trifluoroethoxymethyl oxetane): Multiple crystal phases,crystallization‐induced surface topological complexity and enhanced hydrophobicity

Semicrystalline poly(bis‐trifluoroethoxymethyl)oxetane, P(B‐3FOx), was prepared by cationic ring‐opening polymerization at ?5 °C with M_n up to 21 kDa. Differences in cooling rates from the melt have substantial effects on crystal phase, percent crystallinity, surface topography, and wetting behavior. DSC and WAXD show that cooling from the melt at slow rates (<5 °C/min) gives α‐P(B‐3FOx) with ΔH_f = 22–27 J/g. Quenching from the melt results in β‐P(B‐3FOx) for which a mesophase structure is suggested. β‐P(B‐3FOx) melts at 53 °C followed by recrystallization to α‐P(B‐3FOx). Solution casting from THF results in third phase, γ‐P(B‐3FOx). TM‐AFM and SEM imaging for α‐P(B‐3FOx) showed that cold crystallization at 25 °C brought about increased crystallinity and surface topologies characterized by sharp asperities and lath‐shaped crystals. Spontaneous surface roughening of α‐P(B‐3FOx) results in a discontinuous three‐phase contact line with water and an increase in water sessile drop contact angle from 106° to 136°. The ～30° increase in water contact angle was attributed primarily to a topological change from a relatively smooth surface (Wenzel state) to an asperity‐rich surface yielding a discontinuous three‐phase contact line (composite of Wenzel and Cassie‐Baxter state). The oleophobicity for this polymer, which contains only a single ? CF₃ end group on each side chain, compares favorably with more highly fluorinated acrylates. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1022–1034, 2010     

Easy Access to Modified Cyclodextrins by an Intramolecular Radical Approach

A simple method to modify the primary face of cyclodextrins (CDs) is described. The 6^I‐O‐yl radical of α‐, β‐, and γ‐CDs regioselectively abstracts the H5^II, located in the adjacent D ‐glucose unit, by an intramolecular 1,8‐hydrogen‐atom‐transfer reaction through a geometrically restricted nine‐membered transition state to give a stable 1,3,5‐trioxocane ring. The reaction has been extended to the 1,4‐diols of α‐ and β‐CD to give the corresponding bis(trioxocane)s. The C₂‐symmetric bis(trioxocane) corresponding to the α‐CD is a stable crystalline solid whose structure was confirmed by X‐ray diffraction analysis. The calculated geometric parameters confirm that the primary face is severely distorted toward a narrower elliptical shape for this rim.