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Ab initio molecular orbital calculations at the MP3/6-311+G * //HF /6-311+G * level show that relative energics of TTT, TGT, TTG, GTG, GTG', TGG, TGG', GGG, and GGG' rotamers of 1,2-dimethoxyethane are 0.0, 0.51, 1.65, 3.47, 3.34, 2.24, 0.53, 1.97, and 2.30 kcal/mol, respectively. Populations of rotamers predicted from calculated ΔG's at 273. 15 K agree satisfactorily with the gas-phase electron diffraction results reported by Astrup

Department of Chemistry, UniVersity of LeuVen,Celestijnenlaan 200F, B-3001 LeuVen, Belgium, NationalInstitute of AdVanced Industrial Science and Technology,AIST Tsukuba Central 5, Tsukuba 305-8565, Japan, andDepartment of Information Systems Engineering, Faculty ofEngineering, Osaka Sangyo UniVersity, Daito 574, JapanReceiVed: January 23, 2001; In Final Form: July 5, 2001In this note, we comment on the electronic mechanism ofthe concerted 1,3-dipolar cycloaddition reaction of fulminic acidto acetylene (HCNO + HCCH), which has recently been studiedby valence bond and molecular orbital approaches by fourdifferent groups including ourselves: (i) Sakata, K. J. Phys.Chem. A 2000, 104, 10001, (ii) Harcourt, R. D.; Schulz, A. J.Phys. Chem. A 2000, 104, 6510, (iii) Nguyen, M. T.; Chandra,A. K.; Sakai, S.; Morokuma, K. J. Org. Chem. 1999, 64, 65,and (iv) Karadakov, P. B.; Cooper, D. L.; Gerratt, J. Theor.Chem. Acc. 1998, 100, 222. The main discrepancy arising fromthese theoretical studies concerns the electronic reorganization,and in particular, the direction of the electron flow accompany-ing the nuclear deformation at the transition structure. Wepresent additional results supporting our earlier findings that inthe 1,3-dipolar cycloaddition of fulminic acid (HCNO) andprobably substituted nitrile-oxides (RCNO), to alkynes andphosphaalkynes, the oxygen (O) atom behaves as a bondacceptor center and the carbon (C) as a bond donor.The 1,3-dipolar cycloaddition is a general and powerfulmethod for the synthesis of five-membered heterocyclic com-pounds owing to the great variety and availability of dipolesand dipolarophiles.

The efficient asymmetric total synthesis of (―)-oseltamivir, an antiviral reagent, has been accomplished by using two "one-pot" reaction sequences, with excellent overall yield (60 % ) and only one required purification by column chromatography. The first one-pot reaction sequence consists of a diphenylprolinol silyl ether mediated asymmetric Michael reaction, a domino Michael reaction/ Horner―Wadsworth―Emmons reaction combined with retro-aldol/Horner― Wadsworth―Emmons reaction and retro Michael reactions, a thiol Michael reaction, and a base-catalyzed isomerization. Six reactions can be successfully conducted in the second one-pot reaction sequence; these are deprotection of a tert-butyl ester and its conversion into an acyl chloride then an acyl azide, Curtius rearrangement, amide formation, reduction of a nitro group into an amine, and a retro Michael reaction of a thiol moiety. A column-free synthesis of (—)—oseltamivir has also been established.

The chiral titanium complex-catalyzed ene-type reaction and the Mukaiyama aldol reaction with fluoral are shown to serve as an efficient route to the enantioselective and diastercoselective synthesis of CF 3 -substituted components of biological and synthetic importance.

Phenols were vinylated at the ortho-position with ethyne in the presence of SnCl4−Bu3N reagent. The reaction was applicable to phenols possessing either electron-donating or electron-withdrawing groups. 2,6-Divinylphenols were synthesized under modified conditions. A reaction mechanism involving carbostannylation of alkynyltin and phenoxytin was discussed.

Transport abilities of alkaline earth, transition, and heavy metal ions were examined for three kinds of disubstituted monoacid derivatives of Kemp’s triacid as transport agents for a liquid membrane system. Diamide derivatives showed high transport ability for CaII over MgII, with selectivity ratios greater than 25. Imide monoacids were also CaII selective. For transition and heavy metal ions, all monoacids including diester monoacid showed very high HgII transport, but with different selectivities depending on the functional group. High HgII/AgI ( = 24), HgII/CuII ( = 194), and HgII/PbII ( = 85) selectivities were observed for diamide, diester, and imide monoacids, respectively. The transport mechanisms are discussed for alkaline earth, transition, and heavy metal ions utilizing ion chromatography analysis of anions co-transported.

In the presence of GaCl3, silylethyne reacted electrophilically with aromatic hydrocarbons to give β-silylethenylated arenes. The reaction proceeded via cationic species generated by the interaction of GaCl3 and silylethyne. High reactivity of the intermediate was demonstrated by the rapid reaction rate at −78 °C using close to the equimolar amount of the substrates. ipso-Substitution reaction took place with 1,2,3-trimethoxybenzene. Structures and properties of several organogallium compounds involved in the reactions are discussed.

A method for one-pot preparation of o-xylylene diamine, 1,8-diaminomethylnaphthalene, and 1,2,4,5-tetrakis(aminomethyl)benzene has been developed. The procedure is simpler and the yield of the reaction is higher than by the conventional method

In the attack of OCH 3 − on ethylene phosphate monoanion, a dianionic pentacoordinate intermediate has been found by ab initio calculations at the 3-21 G* level. Although only marginally stable, this contrasts with the results of Lim and Karplus (Nonexistence of Dianionic Pentacovalent Intermediates in the ab Initio Study of the Base-Catalyzed Hydrolysis of Ethylene Phosphate. J. Am. Chem. Soc. 1990, 112, 5872-5873) for attack by OH − on ethylene phosphate monoanion where there is only a pentacoordinate transition state. Together with the results of another paper, it can be concluded that the cause of the discrepancy is attributable to the difference in axial substituents (OCH 3 vs OH)

trans-tert-Butyldimethylsiloxy-L-proline displays greater catalytic activity and affords higher enantioselectivity than the parent proline in the alpha-amination reaction of carbonyl compounds with azodicarboxylate. A quantum mechanical calculation reveals the structure of the transition state. In the presence of a catalytic amount of siloxyproline and water (3-9 equiv), alpha-amino carbonyl derivatives, which are important synthetic intermediates, are obtained in good yield and with excellent enantioselectivity.

trans-tert-Butyldimethylsiloxy-L-proline displays greater catalytic activity and affords higher enantioselectivity than the parent proline in the alpha-amination reaction of carbonyl compounds with azodicarboxylate. A quantum mechanical calculation reveals the structure of the transition state. In the presence of a catalytic amount of siloxyproline and water (3-9 equiv), alpha-amino carbonyl derivatives, which are important synthetic intermediates, are obtained in good yield and with excellent enantioselectivity.

The exo and endo transition structures for the ene reaction of methyl acrylate with propene have been located with RHF calculations at the 3-21G and 6-31G levels. Energetics have been evaluated with the 6-31G* basis set and MP2 correlation energy correction. The transition-state geometries and the calculated energetics have been compared with those for the parent ene reaction between ethylene and propene. The exo and endo transition structures resemble rather closely that for the parent ene reaction. Reasonable substituent effects are indicated on activation energies and extents of electron transfer in the transition states. According to the calculated overlap populations, the transition structures for methyl acrylate ene reaction have less asynchronous character in the bond reorganization as compared with the parent ene reaction. The relatively small stability difference between exo and endo transition structures suggests that intrinsic exo/endo selectivity in the ene reactions is not so obvious as in th...

The CCSD(T) level interaction energies of eight orientations of nitrobenzene-benzene complexes and nine orientations of nitrobenzene dimers at the basis set limit have been estimated. The calculated interaction energy of the most stable slipped-parallel (C(s)) nitrobenzene-benzene complex was -4.51 kcal/mol. That of the most stable slipped-parallel (antiparallel) (C(2h)) nitrobenzene dimer was -6.81 kcal/mol. The interaction energies of these complexes are significantly larger than that of the benzene dimer. The T-shaped complexes are substantially less stable. Although nitrobenzene has a polar nitro group, electrostatic interaction is always considerably weaker than the dispersion interaction. The dispersion interaction in these complexes is larger than that in the benzene dimer, which is the cause of the preference of the slipped-parallel orientation in these complexes.

The CCSD(T) level interaction energies of CH/pi complexes at the basis set limit were estimated. The estimated interaction energies of the benzene complexes with CH(4), CH(3)CH(3), CH(2)CH(2), CHCH, CH(3)NH(2), CH(3)OH, CH(3)OCH(3), CH(3)F, CH(3)Cl, CH(3)ClNH(2), CH(3)ClOH, CH(2)Cl(2), CH(2)FCl, CH(2)F(2), CHCl(3), and CH(3)F(3) are -1.45, -1.82, -2.06, -2.83, -1.94, -1.98, -2.06, -2.31, -2.99, -3.57, -3.71, -4.54, -3.88, -3.22, -5.64, and -4.18 kcal/mol, respectively. Dispersion is the major source of attraction, even if substituents are attached to the carbon atom of the C-H bond. The dispersion interaction between benzene and chlorine atoms, which is not the CH/pi interaction, is the cause of the very large interaction energy of the CHCl(3) complex. Activated CH/pi interaction (acetylene and substituted methanes with two or three electron-withdrawing groups) is not very weak. The nature of the activated CH/pi interaction may be similar to the hydrogen bond. On the other hand, the nature of other typical (nonactivated) CH/pi interactions is completely different from that of the hydrogen bond. The typical CH/pi interaction is significantly weaker than the hydrogen bond. Dispersion interaction is mainly responsible for the attraction in the CH/pi interaction, whereas electrostatic interaction is the major source of attraction in the hydrogen bond. The orientation dependence of the interaction energy of the typical CH/pi interaction energy is very small, whereas the hydrogen bond has strong directionality. The weak directionality suggests that the hydrogen atom of the interacting C-H bond is not essential for the attraction and that the typical CH/pi interaction does not play critical roles in determining the molecular orientation in molecular assemblies.

[reaction: see text] The key [4 + 4] cycloaddition in the biosynthesis of epoxytwinol A has been established by theoretical calculations to comprise of three processes. The first step is formation of the C8-C8' bond generating a biradical intermediate. Next, rotation about the C8-C8' bond occurs, and finally the C1-C1' bond is formed. Biradicals stabilized by conjugation and two hydrogen bonds are essential for realization of this rare thermal [4 + 4] cycloaddition.

The oxidized octaethyltetraphenylporphyrin (1, OETPP) and the corresponding newly prepared octaisobutyltetraphenylporphyrin (3, OisoBuTPP) could be isolated from the reaction of OETPPLi2 (or OisoBuTPPLi2) with SOCl2. The X-ray analysis and the characteristic UV-vis spectra of 1 and 3 revealed that these are the first examples of 16 pi nonaromatic porphyrins.

The intermolecular interaction energy of the toluene dimer has been calculated with the ARS-F model (a model chemistry for the evaluation of intermolecular interaction energy between ARomatic Systems using Feller's method), which was formerly called as the AIMI model III. The CCSD(T) (coupled cluster calculations with single and double substitutions with noniterative triple excitations) interaction energy at the basis set limit has been estimated from the second-order Moller-Plesset perturbation interaction energy at the basis set limit obtained by Feller's method and the CCSD(T) correction term obtained using a medium-size basis set. The cross (C(2)) dimer has the largest (most negative) interaction energy (-4.08 kcal/mol). The antiparallel (C(2h)) and parallel (C(S)) dimers (-3.77 and -3.41 kcal/mol, respectively) are slightly less stable. The dispersion interaction is found to be the major source of attraction in the toluene dimer. The dispersion interaction mainly determines the relative stability of the stacked three dimers. The electrostatic interaction of the stacked three dimers is repulsive. Although the T-shaped and slipped-parallel benzene dimers are nearly isoenergetic, the stacked toluene dimers are substantially more stable than the T-shaped toluene dimer (-2.62 kcal/mol). The large dispersion interaction in the stacked toluene dimers is the cause of their enhanced stability.

The properties of supercritical fluid carbon dioxide were predicted satisfactorily by molecular dynamics simulations using a model potential from ab initio calculations. The model potential was obtained from the interaction energies of dimers calculated at the MP2/6-311 + G(2df)-level. The pressures and self-diffusion coefficients calculated by the simulations for the NVT ensembles reproduce the experimental values.

The intermolecular interaction energies of naphthalene dimers have been calculated by using an aromatic intermolecular interaction model (a model chemistry for the evaluation of intermolecular interactions between aromatic molecules). The CCSD(T) (coupled cluster calculations with single and double substitutions with noniterative triple excitations) interaction energy at the basis set limit has been estimated from the second-order Møller-Plesset perturbation interaction energy near saturation and the CCSD(T) correction term obtained using a medium-size basis set. The estimated interaction energies of the set of geometries explored in this work show that two structures emerge as being the lowest energy, and may effectively be considered as isoenergetic on the basis of the errors inherent in out extrapolation procedure. These structures are the slipped-parallel (Ci) structure (-5.73 kcal/mol) and the cross (D2d) structure (-5.28 kcal/mol). The T-shaped (C2v) and sandwich (D2h) dimers are substantially less stable (-4.34 and -3.78 kcal/mol, respectively). The dispersion interaction is found to be the major source of attraction in the naphthalene dimer. The electrostatic interaction is substantially smaller than the dispersion interaction. The large dispersion interaction is the cause of the large binding energies of the cross and slipped-parallel dimers.

The intermolecular interaction energy curves of CH(3)OCH(3)-CH(2)F(2), CF(3)OCH(3)-CH(2)F(2), CF(3)OCF(3)-CH(2)F(2), CH(3)OCH(3)-CHF(3), CF(3)OCH(3)-CHF(3), and CF(3)OCF(3)-CHF(3) complexes were calculated by the MP2 level ab initio molecular orbital method using the 6-311G** basis set augmented with diffuse polarization functions. We investigate the fluorine substitution effects of both methane and dimethyl ether on intermolecular interactions. In addition, orientation dependence of intermolecular interaction energies is also studied with utilizing eight types of orientations. Our analyses demonstrate that partial fluorinations of methane make electrostatic interaction dominant, and consequently enhance attractive interaction at several specific orientations. On the contrary, fluorine substitutions of dimethyl ether substantially decrease the electrostatic interaction between ether and CH(2)F(2) or CHF(3); thus, there is no such characteristic interaction between the C-H of fluorinated methane and ether oxygen of CF(3)OCF(3) as conventional hydrogen bonding, due to reduced polarity of fluorinated ether. The combination of different pairs of the electrostatic interaction is therefore responsible for the intermolecular interaction differences among the complexes investigated herein and also their orientations.

Hydrogen bond complex stability between adenine (A) and hydrogen bond equivalents of uracil: 2-pyridone derivatives (U(X2O)X) and 3-oxo-1,2,6-thiadiazine-1,1-dioxide derivatives (U(SO2)X) was studied, and as the result, the hydrogen bond energy of U(X2O)X-A and a complex of UX(SO2)X-A, was about 1.5 kcal/mol more stable than that of the corresponding adenine-uracil derivatives complex, respectively. The energy difference between the imide tautomer and enol tautomer was smaller than those of uracil derivatives. U(SO2)F can form a stable complex with A, and its imide tautomer is stable.

The substitution effect on hydrogen bond stability of the Watson-Crick type base pair between 1-methylcytosine (C) and substitution-introduced 9-methylguanine derivatives (Gx) was studied by an ab initio molecular orbital theory. Introduction of an electron-withdrawing group on the 8-position or on the exo-cyclic amino moiety enforced the base pair stability.

Systematic substituent effects on the stability of the hydrogen bonding between substituted 9-methyladenine derivatives (Ax) and 1-methyluracil (U) were studied by ab initio molecular orbital theory. Predicted substituent effects on the hydrogen bond energies of Ax-U base pairs were in good agreement with those observed for experimental binding constants. Ab initio calculation is effective for evaluation of the stability of the hydrogen-bonding pairs of chemically modified nucleic acid base analogues. In contrast to the substitution effect of uracil on hydrogen bond energies of A-Ux base pairs, it is difficult to systematically interpret the substitution effect of adenine derivatives for Ax-U base pairs.

The substitution effect on hydrogen bond energy of the Watson-Crick type base pair between 9-methylguanine (G) and chemically modified 1-methylcytosine (CX) derivatives was evaluated by ab initio molecular orbital theory. A remarkable trend was observed in the substitution effect of the hydrogen bond stability: Cytosine derivatives possessing an electron-donating group form stable base pairs with guanine. However, both the hydrogen bond distance and the charge distribution were not good indexes for the hydrogen bond status in CX-G base pairing.

The accurate O-H bond dissociation enthalpies for a series of meta and para substituted phenols (X-C 6 H 4 -OH, X=H, F, Cl, CH 3 , OCH 3 , OH, NH 2 , CF 3 , CN, and NO 2 ) have been calculated by using the (RO)B3LYP procedure with 6-311G(d,p) and 6-311++G(2df,2p) basis sets. The proton affinities of the corresponding phenoxide ions (X-C 6 H 4 -O - ) have also been computed at the same level of theory. The effect of change of substituent position on the energetics of substituted phenols has been analyzed. The correlations of Hammett’s substituent constants with the bond dissociation enthalpies of the O-H bonds of phenols and proton affinities of phenoxide ions have been explored. Keywords: Substituted Phenol, Bond Dissociation Energy, Acidity, DFT. I. Introduction Phenols are widely used as synthetic organic materials and also as antioxidants in living organisms [1]. Phenoxyl radicals are known as important intermediates in many biological and industrial applications [2]. Phenols are of special interest in organic chemistry, since their acid-base equilibria have often been used as reference values in establishing linear free energy relationships [3]. Consequently, much effort has been put to understand the factors governing the O-H bond dissociation energies, BDE(O-H), and acidities of substituted phenols, both in the solution and gas phase [4-11].

The conformation and vibrational properties of 2-methoxy-1,2-diphenylethanone (MDPE) are investigated in the gas phase and in organic solvents. Ab initio calculations carried out at the B3LYP/6-31G(d) level demonstrate that three stable conformers having cisoid, skewed and transoid structures are present in the gas phase. In the gas phase, the conformers are separated by a low energy barrier and their relative energies do not differ by more than 7.2 kJ mol (-1) Like in crystalline MDPE 'Acta Crystallogr. Sect. C 44 (1988) 894', weak CH...O hydrogen bonds are present in the cisoid conformation. The IR and Raman spectra of solid MDPE are discussed. Several vibrational modes are split in organic solvents. A comparison between the theoretical data and the experimental dipole moments indicates that two conformers are present in solution, the population of the cisoid form increasing with the permittivity of the medium.

A model chemistry for the evaluation of intermolecular interaction between aromatic molecules (AIMI Model) has been developed. The CCSD(T) interaction energy at the basis set limit has been estimated from the MP2 interaction energy near the basis set limit and the CCSD(T) correction term obtained by using a medium size basis set. The calculated interaction energies of the parallel, T-shaped,and slipped-parallel benzene dimers are -1.48, -2.46, and -2.48 kcal/mol, respectively. The substantial attractive interaction in benzene dimer, even where the molecules are well separated, shows that the major source of attraction is not short-range interactions such as charge-transfer but long-range interactions such as electrostatic and dispersion. The inclusion of electron correlation increases attraction significantly. The dispersion interaction is found to be the major source of attraction in the benzene dimer. The orientation dependence of the dimer interaction is mainly controlled by long-range interactions. Although electrostatic interaction is considerably weaker than dispersion interaction, it is highly orientation dependent. Dispersion and electrostatic interactions are both important for the directionality of the benzene dimer interaction.

The energies, vibrational frequencies and IR intensities of cis - and trans - N -acetyl- l -alanine (NAAL) are computed using the density functional theory (B3LYP) combined with the 6-311G(d, p) basis set. The trans conformer is characterized by an intramolecular NH ... O hydrogen bond leading to the formation of a five-membered ring and is by 23 kJ mol −1 more stable than the cis conformer. The difference between the vibrational frequencies and IR intensities computed for the two conformers is discussed. The IR spectra at different temperatures and the Raman spectra of solid NAAL and its deuterated counterpart are investigated and discussed. The frequencies of the ν (OH) vibration and the isotopic ratio suggest the formation of short OH ... O hydrogen bonds in the solid state. The NH group seems also to be involved in a weak hydrogen bond.

Pathways for hydrogen abstraction (H-abstraction) by the NO3 radical from the SH and the CH sites of the CH3SH molecule have been found for the reaction of CH3SH + NO3. Energy evaluations of the st...

Chemical cross-linking reaction, although rather simple as a principle, is a powerful tool for processing polymeric materials, since it can significantly alter the molecular structure of materials as a whole, even if the alteration of the structural unit might be little. This situation — the properties of cross- linked materials could significantly differ from those of the original polymers — could be compared to the fact that the properties of polymers significantly differ from those of their monomers.

The oxidized octaethyltetraphenylporphyrin (1, OETPP) and the corresponding newly prepared octaisobutyltetraphenylporphyrin (3, OisoBuTPP) could be isolated from the reaction of OETPPLi2 (or OisoBuTPPLi2) with SOCl2. The X-ray analysis and the characteristic UV-vis spectra of 1 and 3 revealed that these are the first examples of 16 pi nonaromatic porphyrins.

The enzymatic cleavage of RNA takes place via a cyclic pentacoordinate oxyphosphorane intermediate/transition state. We carried out ab initio investigations on the neutral cyclic oxyphosphorane, which exists as a stable intermediate. As a consequence of the conformational preferences of the pentacoordinate trigonal bipyramidal intermediates, the rotation of the P-OH bonds is strongly coupled with the reaction coordinate for the pseudorotation process. In addition, the neutral PF(4)OH species has a higher barrier to pseudorotation than the corresponding anionic species PF(4)O(-). These findings are related to the positive charge of the hydrogen atoms on the equatorial oxygens in the trigonal bipyramidal structures: the hydrogen atoms preferably adopt eclipsed positions relative to the axial ligands. Fixing the cationic species in these regions causes an increase in the barrier heights for pseudorotation processes and, thus, prevents isomerization by pseudorotation. Consequently, metal coordination in the double-metal ion mechanism for enzymatic cleavage of RNA should serve to exclusively stabilize the trigonal bipyramidal intermediate/transition state for the in-line attack and departure process.

We have developed a new organic synthesis design system named CASINO ( C omputer- A ided S ynthesis IN ference for O rganic Compounds). CASINO is a comprehensive hybrid system with various functions required for synthesis design. The present work describes three main modules of CASINO, the modules for generation of reaction sequences, chiral synthon recognition, and retrosynthetic analysis.

From calculations of a model reaction scheme for base-catalyzed RNA hydrolysis (which also represents the base-catalyzed methanolysis of ethylene phosphate monoanion in reverse), a pentacoordinate dianionic intermediate 2a (Storer et al. J. Am. Chem. Soc. 1991, 113, 5216-5219) as well as two transition states, TS1 and TS2, to the intermediate have been located by ab initio calculations at the 3-21G* level. However, the intermediate, which has a well depth on the order of k(B)T, is unlikely to be kinetically significant. The endocyclic P-O(2') bond is found to be much weaker than the exocyclic P-O(5') bond. In agreement with this finding, calculations on 2a at the 6-31+G* level abolishes TS1 and the pentacoordinate intermediate, leaving only TS2 as the sole transition state. Thus, for all the cases examined, the rate-limiting transition-state structure is TS2 which has an extended P-O(5') breaking bond. These results and the mode of cleavage of a simpler compound 3b are in accord with stereoelectronic predictions (see text for the definition). Moreover, solvation appears to stabilize the pentacoordinate intermediate. In the gas phase, the simplest oxyphosphorane 3b has the least tendency to form a pentacoordinate intermediate. However, 3b does form a pentacoordinate intermediate when it is solvated with six water molecules. These results support the hypothesis that phosphoryl-transfer reactions take place via pentacoordinate intermediates not only in acidic but also in basic media.

To elucidate the role of the Mg2+ ion in ribozyme reactions, we carried out ab initio molecular orbital investigations on dianionic trimethoxyphosphorane A and its Mg2+ complex (overall a neutral molecule) as a model system for the reaction center of Tetrahymena-type ribozyme. Although dianionic oxyphosphorane A concentrates its negative charges on the equatorial phosphoryl oxygens, the coordination of the Mg2+ ion between these two oxygens is unlikely. Geometry optimizations of the complex and the electrostatic potential of A both suggest that Mg2+ coordination preferably occurs in the region between the axial oxygen and the equatorial phosphoryl oxygen. The considerations of electrostatic potential rationalize the geometries of carboxylate-metal and phosphate-metal interactions extracted from the Cambridge Structural Database as well. Consequently, the Mg2+ ion at the active site of Tetrahymena-type ribozyme most likely lies in the regions between the axial and equatorial oxygens. The axial-equatorial coordinations of Mg2+ ions conceivably increase the electronegativities of the axial oxygens and facilitate cleavage of the phosphodiester bond located at the junction of the intron and the exon. It is thus likely that the Mg2+ ions play the key role in the phosphodiester cleavage reactions mediated by ribozymes.

Multistep fluorescence resonance energy transfer in a system containing three chromophores is dependent upon the relative arrangement of the chromophore triad.

From calculations of a model reaction scheme for base-catalyzed RNA hydrolysis, a pentacoodinate dianionic intermediate 2a (Storer, et al., J. Am. Chem. Soc. , 1991 , 113 , 5216–5219) as well as two transition state, TS1 and TS2 , to the intermediate have been locateed by ab initio calculations at the 3–21G ∗ level. Although the intermediate, which has the well depth on the order of k B T, is unlikely to be kinetically significant, the overall rate-limiting transition state structure TS2 obtained at 3–21G ∗ level is very close to the corresponding structure at the STO-3G level; it has an extended P-O(5′) bond breaking character. These gas-phase calculation results are used to qualitatively interpret mutagenesis results of Barnase and RNase T 1 where water molecules are absent from the active site.

In order to examine the energetics in base-catalyzed hydrolysis of RNA, a tentative pentacoordinated intermediate (3) has been characterized by molecular orbital calculations. Ab initio studies at the level of 3-21G* indicate that, under the Cs symmetry restricted conditions, the P-O(2) bond possessing antiperiplanar (app) lone pair electrons (Ip) on the equatorial oxygen (O(3)) can be cleaved with almost no barrier (TS1 transition state; 0.08 kcal mol-1), from the pentacoordinated intermediate (3) of base-catalyzed hydrolysis of phosphate, compared to the P-O(5) bond (TS2 transition state; 28.9 kcal mol-1) which lacks app lp assistance from O(3). The dianionic intermediate, however, loses the TS1 transition state thus its property as an intermediate when the Cs restriction is removed. The analysis of the entire potential energy surface enables us to conclude that, in a related system examined by Lim and Karplus [1990) J. Am. Chem. Soc., 112, 5872-5873) for attack by OH- on ethylene phosphate monoanion, the TS1 transition state had also been lost and thus no intermediate had been found. These results further support our earlier conclusions (Taira et al. (1990) Protein Engineering, 3, 691-701) of rate limiting transition state possessing extended P-O(5') bond breaking character (the TS2 transition state) in the base-catalyzed hydrolysis of RNA. Finally, although the lack of 2',3' -migration of phosphate moieties in basic condition appears to be in accord with the short-lived intermediate, it really does not prove the absence of the intermediate. The detail will be discussed in the text.

We prepared a series of ligands possessing two binding sites for metal coordination: in each ligand molecule, two binding sites with the same functionality (2,2'-dipicolylamino group) were placed at the of various methyl arenes. Thus, the distances between the metal binding sites were different from ligand to ligand. We examined the rate of the hydrolysis of RNA dimer catalyzed by La3+ ion binuclear complexes of the ligands. The catalytic activity of the binuclear complexes increased as the distance between the metal binding sites was decreased.

Geometries and interaction energies for methane clusters with naphthalene and pyrene were studied. Estimated CCSD(T) interaction energies for the clusters at the basis set limit were -1.92 and -2.50 kcal mol(-1), respectively. Dispersion is mainly responsible for the attraction. Electrostatic interaction is very small. Although the benzene-methane cluster prefers a monodentate structure, in which a C-H bond of the methane points toward the benzene, the methane clusters with the polycyclic aromatic hydrocarbons do not prefer monodentate structures. In the benzene-methane cluster, the weak electrostatic interaction stabilizes the monodentate structure. On the other hand the dispersion interaction controls the orientation of methane in the naphthalene and pyrene clusters. The dispersion interactions in these clusters are significantly larger than those in the benzene-methane cluster. The methane prefers the orientation which is suitable for stabilization by dispersion. Hydrogen atoms of the methane locate above the centers of hexagonal rings of the polycyclic aromatic hydrocarbons in the stable structures. The structures have a small steric repulsion and this positions them only a short distance from the aromatic plane. The large dispersion contribution to the attraction shows that interactions between carbon atoms are mainly responsible for the attraction, and that hydrogen atoms are not important for the attraction. This shows that the interactions between the methane and polycyclic aromatic hydrocarbons are not pi-hydrogen bonds.