Aspartic acid side chain effect—Experimental and theoretical insight

Gas-phase H/D exchange and density functional theory study of the Asp and Glu side-chain carboxylic group intrinsic reactivity is reported. H/D exchange site specific treatment and some additional theoretical calculations showed that a side-chain carboxylic group may initiate proton transfer along with bond formation to one of its oxygens, i.e., possibility to initiate selective of cleavage peptide bond ("aspartic acid effect"). That finding is used to select aspartic acid cleavage mechanisms (side-chain proton transfer either to backbone carbonyl or to amide nitrogen) for further computational study. B3LYP/6-31G(d) and G3(MP2)//B3LYP potential energy profiles of both mechanisms on a model system CH3CO-Asp-NHCH3 were constructed. Although energy employed in low-energy collision induced dissociation suffices for both mechanisms thresholds, energy transferred to specific modes suggests a complex one-step mechanism of proton transfer (from the side-chain carboxylic group to the backbone amide group), bond formation (between deprotonated carboxylic group and carbon atom of the backbone carbonyl), and peptide bond cleavage as favorable.     

过渡金属异核原子簇化学键研究 1: Ⅷ-Ⅷ, ⅥB-Ⅷ族双金属原子簇电子结构研究

本文对18个Ⅷ族双金属四面体簇和16个ⅥB-Ⅷ异金属四核簇进行了量子化学研究, 用DV-Xα方法讨论了它们的化学键、电荷转移、能级态密度。计算结果表明: Ⅷ族四面体簇需36个金属电子, 其中12个形成6个金属簇骼轨道, 24个与配体成键; ⅥB-Ⅷ异金属簇核中, 因两金属能带、电负性差异, ⅥB原子易向Ⅷ原子转移电荷, 环戊二烯基配体促进这一过程; 异金属簇能级总价带比单金属簇收缩, 而d能带比单金属簇展宽。     

QM/MM study of mechanisms for compound I formation in the catalytic cycle of cytochrome P450cam

In the catalytic cycle of cytochrome P450cam, after molecular oxygen binds as a ligand to the heme iron atom to yield a ferrous dioxygen complex, there are fast proton transfers that lead to the formation of the active species, Compound I (Cpd I), which are not well understood because they occur so rapidly. In the present work, the conversion of the ferric hydroperoxo complex (Cpd 0) to Cpd I has been investigated by combined quantum-mechanical/molecular-mechanical (QM/MM) calculations. The residues Asp(251) and Glu(366) are considered as proton sources. In mechanism I, a proton is transported to the distal oxygen atom of the hydroperoxo group via a hydrogen bonding network to form protonated Cpd 0 (prot-Cpd0: FeOOH(2)), followed by heterolytic O-O bond cleavage that generates Cpd I and water. Although a local minimum is found for prot-Cpd0 in the Glu(366) channel, it is very high in energy (more than 20 kcal/mol above Cpd 0) and the barriers for its decay are only 3-4 kcal/mol (both toward Cpd 0 and Cpd I). In mechanism II, an initial O-O bond cleavage followed by a concomitant proton and electron transfer yields Cpd I and water. The rate-limiting step in mechanism II is O-O cleavage with a barrier of about 13-14 kcal/mol. According to the QM/MM calculations, the favored low-energy pathway to Cpd I is provided by mechanism II in the Asp(251) channel. Cpd 0 and Cpd I are of similar energies, with a slight preference for Cpd I.     

Weak metal-metal bonding in small manganese cluster ions, Mn(N)+ (N < or = 7)

The binding energies of manganese cluster ions Mn(N)+ (N = 5-7) were determined by the photodissociation experiments in the near-infrared and visible-photon-energy ranges. The bond dissociation energies of Mn(N)+, D0(Mn(N-1)+...Mn), were obtained to be 1.70+/-0.08, 1.04+/-0.10, and 1.46+/-0.11 eV, respectively, for N = 5, 6, and 7 from the threshold energies for the two-atom loss processes and the bond dissociation energies of Mn3(+) and Mn4(+) reported previously [A. Terasaki et al., J. Chem. Phys. 117, 7520 (2002)]. Correspondingly, binding energies per atom are obtained to be 0.99+/-0.03, 1.00+/-0.03, and 1.06+/-0.03 eV/at. for N = 5, 6, and 7, respectively. A gradual increase in the binding energy from N = 2 to N = 7 shows an increasing contribution of nonbonding 3d orbitals to the bonding via weak hybridization with valence 4s orbitals as the cluster size increases. These binding energies per atom are still much smaller than the bulk cohesive energy of manganese (2.92 eV/at.), and this finding indicates exceptionally weak metal-metal bonds in this size range.     

The importance of lone pair delocalizations: theoretical investigations on the stability of cis and trans isomers in 1,2-halodiazenes

The relative and thermodynamic stabilities of cis and trans isomers of 1,2-dihalodiazenes (XN=NX; X = F, Cl, or Br) were examined using high level ab initio and density functional theory (DFT) calculations. For 1,2-dihalodiazenes, it was found that the cis isomers were more stable than the corresponding trans isomers, despite the existence of several cis destabilizing mechanisms, such as steric exchange between halogen lone pairs and dipole-dipole electrostatic repulsions (Delta(trans-cis) = 3.15, 7.04, and 8.19 kcal mol(-1), respectively, at BP86/6-311++G(3df,3pd)//B3LYP /6-311++G(3df,3pd) level). Their origin of the cis-preferred difference in energy was investigated with natural bond orbital (NBO) analysis to show that the "cis effect" came mainly from antiperiplanar interactions (AP effect) between the nitrogen lone pair and the neighboring antibonding orbital of the N-X bond (n(N) --> sigma(N'X'*)). The delocalization of halogen lone-pair into the antibonding orbital of the N=N bonds (the LP effects) was also found to enhance the cis preference by 1.20 to 6.58 kcal mol(-1), depending on the substituted halogen atom. The total amount of the AP effect increased as the halogen atom became larger, and the increased AP effect promoted the triple-bond-like nature of the N=N bond (shorter N=N bond length and wider NNX angle). The greater AP effect also made the N'-X' bond easier to cleave (longer N-X bond length), and a higher energy level than that of the nitrogen lone pair was found in the N-Br bonding orbital in 1,2-dibromodiazenes, thus indicating the significant instability of this molecule. The degradability of the N-Cl bond in 1,2-dichlorodiazenes and the fair stability of the N-F bond in 1,2-fluorodiazenes were also confirmed theoretically, and were found to be consistent with the previous experimental and theoretical reports. These results clearly indicate the dominance of lone-pair-related hyperconjugations on the basic electronic structure and energetic natures of 1,2-dihalodiazene systems.     

Mechanism of C[bond]H bond activation/C[bond]C bond formation reaction between diazo compound and alkane catalyzed by dirhodium tetracarboxylate

The B3LYP density functional studies on the dirhodium tetracarboxylate-catalyzed C-H bond activation/C-C bond formation reaction of a diazo compound with an alkane revealed the energetics and the geometry of important intermediates and transition states in the catalytic cycle. The reaction is initiated by complexation between the rhodium catalyst and the diazo compound. Driven by the back-donation from the Rh 4d(xz) orbital to the C[bond]N sigma*-orbital, nitrogen extrusion takes place to afford a rhodium[bond]carbene complex. The carbene carbon of the complex is strongly electrophilic because of its vacant 2p orbital. The C[bond]H activation/C[bond]C formation proceeds in a single step through a three-centered hydride transfer-like transition state with a small activation energy. Only one of the two rhodium atoms works as a carbene binding site throughout the reaction, and the other rhodium atom assists the C[bond]H insertion reaction. The second Rh atom acts as a mobile ligand for the first one to enhance the electrophilicity of the carbene moiety and to facilitate the cleavage of the rhodium[bond]carbon bond. The calculations reproduce experimental data including the activation enthalpy of the nitrogen extrusion, the kinetic isotope effect of the C[bond]H insertion, and the reactivity order of the C[bond]H bond.     

Detection of OH radical in laser induced photodissociation of tetrahydrofuran at 193 nm

On excitation at 193 nm, tetrahydrofuran (THF) generates OH as one of the photodissociation products. The nascent energy state distribution of the OH radical was measured employing laser induced fluorescence technique. It is observed that the OH radical is formed mostly in the ground vibrational level, with low rotational excitation (approximately 3%). The rotational distribution of OH (v"=0,J) is characterized by rotational temperature of 1250+/-140 K. Two spin-orbit states, 2Pi3/2 and 2Pi1/2 of OH are populated statistically. But, there is a preferential population in Lambda doublet levels. For all rotational numbers, the 2Pi+(A') levels are preferred to the 2Pi-(A") levels. The relative translational energy associated with the photoproducts in the OH channel is calculated to be 17.4+/-2.2 kcal mol-1, giving an fT value of approximately 36%, and the remaining 61% of the available energy is distributed in the internal modes of the other photofragment, i.e., C4H7. The observed distribution of the available energy agrees well with a hybrid model of energy partitioning, predicting an exit barrier of approximately 16 kcal mol-1. Based on both ab initio molecular orbital calculations and experimental results, a plausible mechanism for OH formation is proposed. The mechanism involves three steps, the C-O bond cleavage of the ring, H atom migration to the O atom, and the C-OH bond scission, in sequence, to generate OH from the ground electronic state of THF. Besides this high energy reaction channel, other photodissociation channels of THF have been identified by detecting the stable products, using Fourier transform infrared and gas chromatography.     

Reactivity of alkyl versus silyl peroxides. The consequences of 1, 2-silicon bridging on the epoxidation of alkenes with silyl hydroperoxides and bis(trialkylsilyl)peroxides

The bond dissociation energies for a series of silyl peroxides have been calculated at the G2 and CBS-Q levels of theory. A comparison is made with the O-O BDE of the corresponding dialkyl peroxides, and the effect of the O-O bond strength on the activation barrier for oxygen atom transfer is discussed. The O-O bond dissociation enthalpies (DeltaH(298)) for bis (trimethylsilyl) peroxide (1) and trimethylsilyl hydroperoxide (2) are 54.8 and 53.1 kcal/mol, respectively at the G2 (MP2) and CBS-Q levels of theory. The O-O bond dissociation energies computed at G2 and G2(MP2) levels for bis(tert-butyl) peroxide and tert-butyl hydroperoxide are 45.2 and 48.3 kcal/mol, respectively. The barrier height for 1,2-methyl migration from silicon to oxygen in trimethylsilyl hydroperoxide is 47.9 kcal/mol (MP4//MP2/6-31G). The activation energy for the oxidation of trimethylamine to its N-oxide by bis(trimethylsilyl) peroxide is 28.2 kcal/mol (B3LYP/6-311+G(3df,2p)// B3LYP/6-31G(d)). 1,2-Silicon bridging in the transition state for oxygen atom transfer to a nucleophilic amine results in a significant reduction in the barrier height. The barrier for the epoxidation of E-2-butene with bis(dimethyl(trifluoromethyl))silyl peroxide is 25.8 kcal/mol; a reduction of 7.5 kcal/mol relative to epoxidation with 1. The activation energy calculated for the epoxidation of E-2-butene with F(3)SiOOSiF(3) is reduced to only 2.2 kcal/mol reflecting the inductive effect of the electronegative fluorine atoms.     

Theoretical Investigation on the Geometries and Properties of Guanine-BX3 （X = F, Cl） Complex

Geometries and binding energies were predicted at the B3LYP/6-311+G* level for the guanine-BX3 (X = F, Cl) systems and four isomers with no imaginary frequencies have been obtained for both guanine-BF3 and guanine-BCl3, respectively. Single energy calculations using much larger basis sets (6-311+G(2df,p) and aug-cc-pVDZ were carried out as well. It was found that the most stable isomer of guanine-BF3 is BF3 connected to N3 of guanine with the stabilization energy of –19.93 kcal/mol (BSSE corrected), while that of guanine-BCl3 is BCl3 connected to O10 of guanine having stabilization energy of –15.02 kcal/mol at the same level. The analyses for the combining interaction between BX3 and guanine with the atom-in-molecules theory (AIM) and natural bond orbital (NBO) methods have been performed. The results indicated that all the isomers are formed with σ-p type interactions between guanine and BX3, in which pyridine-type nitrogen or carbonyl oxygen or nitrogen atom of amino group offers its lone pair electrons to the empty p orbital of boron atom and the concomitance of charge transfer from guanine to BX3 has occurred. Still, one or two hydrogen bonds exist in some isomers of guanine-BX3 system and contribute to the stability of complex systems. Frequency analysis suggested that the stretching vibration of BX3 undergoes a red shift in complexes. Guanine-BF3 complex is more stable than guanine-BCl3 although the B–Y (Y=N, O) bond distance in the latter is shorter.     

Anilinolysis of Picryl Benzoate Derivatives in Methanol: Reactivity,Regioselectivity, Kinetics,and Mechanism

The reaction of picryl benzoate derivatives 1a–g with aniline in methanol proceeds through CO? O and Ar? O bond cleavage pathways. Furthermore, the reactivity of these esters toward anilinolysis is correlated to the energy gap between highest occupied molecular orbital aniline and lowest unoccupied molecular orbital of each ester. The regioselectivity of acyl? oxygen versus aryl? oxygen cleavage is also discussed. The overall rate constants k_tot split into k_{CO? O} (the rate constant of acyl‐oxygen cleavage) and k_{Ar? O} (rate constant of aryl‐oxygen cleavage). The CO? O bond cleavage advances through a stepwise mechanism in which the formation of the tetrahedral intermediate is the rate‐determining step. The Ar? O bond cleavage continues through a S_NAr mechanism in which the departure of the leaving group from the Meisenheimer complex occurs rapidly after its formation in the rate‐determining step.     

碳原子价轨道电负性对化学键性能的影响

研究了同一类型化学键X―C的键能、键长和H―C键的酸性等性能与碳原子价轨道电负性的定量关系。结果表明,X―C键能随碳原子价轨道电负性增加而线性增大;H―C与C―C键的键长随碳原子价轨道电负性增加而线性减小;H―C的酸性随碳原子价轨道电负性增加而线性增大。因而,对结构类似的有机化合物,可以采用碳原子价轨道电负性对实验测定的化学键性能作图,判断其测定结果正确与否。     

Selective mixed coupling of carboxylic acids (II). — photolysis of unsymmetrical diacylperoxides with alkenyl-, halo-, keto-, carboxyl-groups and a chiral α-carbon. Comparison with the mixed kolbe electrolysis

Alkenoyl and functionalized alkanoyl dodecanoyl peroxides are prepared in 70 to 97 % yield and photolyzed at ?78° C. Thereby 4- to 10-alkenoyl and 4-alkanoyl peroxides afford good yields (56 – 68 %) of unsymmetrical coupling products. Similarly α- to σ-haloalkanoyl, cholanoyl or 3- and 4-carboxyalkanoyl peroxides can be coupled (40 – 70 %). The α-chiral diacyl peroxide ls undergoes the photochemical coupling reaction with 80 % retention of its configuration. The photolysis of diacyl peroxides at ?78° C proves to be a favorable supplement of the Kolbe-electrolysis in cases, where the electrolysis fails or produces low yields.     

Free radical abstraction of H atom from peroxides with concerted dissociation of O-O bond

Quantum chemical calculations of the dissociation energy of the C-H bond in the ??-hydroperoxide fragment of Me₂CHOOH were carried out. It was shown that abstraction of H atom is accompanied by dissociation of the O-O bond. Density functional calculations of transition states of the reactions of ^·CH₃, CH₃OO^·, and HO₂ ^· radicals with the C-H bond in the ??-hydroperoxide fragment of Me₂CHOOH were carried out. It was established that H atom abstraction is accompanied by concerted dissociation of the O-O bond. For 45 peroxides R¹R²CHOOH, R¹R²CHOOR³, and R¹R²CHOOC(O)R³ (R¹, R² = H, Me, Et, Ph, H₂C=CH), the enthalpies of H atom abstraction from the C-H bond in the a-hydroperoxide fragment with fragmentation of the peroxides at the O-O bond were calculated. The kinetic parameters for 12 classes of radical abstraction reactions with fragmentation of molecules were calculated from experimental data within the framework of the model of intersecting parabolas. The activation energies and reaction rate constants of H atom abstraction from C-H bonds of a-peroxide fragments involving peroxyl and alkyl radicals were determined for 45 peroxides of different structure.     

Energetics of the manganese oxide cluster cations Mn(N)O+ (N = 2-5): role of oxygen in the binding of manganese atoms

The photodissociation of manganese oxide cluster cations Mn(N)O+ (N = 2-5), into Mn(N-1)O+ (one-atom loss) and Mn(N-2)O+ (two-atom), was investigated in the photon-energy range of 1.08-2.76 eV. The bond-dissociation energies D0(Mn(N-1)O+...Mn) for N = 3, 4, and 5 were determined to be 1.84+/-0.03, 0.99+/-0.05, and 1.25+/-0.14 eV, respectively, from the threshold energies for the one- and two-atom losses. As Mn2O+ did not dissociate even at the highest photon energy used, the bond dissociation energy of Mn2O+, D0(Mn+...MnO), was obtained from a density-functional-theory calculation to be 3.04 eV. The present findings imply that the core ion Mn2O+ is bound weakly with the rest of the manganese atoms in Mn(N)O+.     

Electron structure and reactivity of organofluorine compounds. 3. Mndo and ami calculations of the ground state of perfluoroalkyl chlorides,bromides, and iodides

The semiempirical quantum chemical MNDO and AMI methods were used to determine the equilibrium geometries and electron properties of molecules of perfluoroalkyl halides (R_FX): CF₃X, CF₃CF₂X, (CF₃)₂CFX, (CF₃)₃CX for X=Cl, Br, and I. It was determined that the effective charge on the Cl atom in R_FCl is negative, positive on the I atom in R_FI, and depends on R_F for the Br atom in R_FBr. The CF₃ group can act as either an electron acceptor or donor in various perfluoroalkyl halides. The strongest C–I bond in the perfluoroalkyl halides occurs with a tertiary RF group.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 5, pp. 1059–1063, May, 1990.     

The role of excited Rydberg States in electron transfer dissociation

Ab initio electronic structure methods are used to estimate the cross sections for electron transfer from donor anions having electron binding energies ranging from 0.001 to 0.6 eV to each of three sites in a model disulfide-linked molecular cation. The three sites are (1) the S-S sigma(*) orbital to which electron attachment is rendered exothermic by Coulomb stabilization from the nearby positive site, (2) the ground Rydberg orbital of the -NH(3)(+) site, and (3) excited Rydberg orbitals of the same -NH(3)(+) site. It is found that attachment to the ground Rydberg orbital has a somewhat higher cross section than attachment to either the sigma orbital or the excited Rydberg orbital. However, it is through attachment either to the sigma(*) orbital or to certain excited Rydberg orbitals that cleavage of the S-S bond is most likely to occur. Attachment to the sigma(*) orbital causes prompt cleavage because the sigma energy surface is repulsive (except at very long range). Attachment to the ground or excited Rydberg state causes the S-S bond to rupture only once a through-bond electron transfer from the Rydberg orbital to the S-S sigma(*) orbital takes place. For the ground Rydberg state, this transfer requires surmounting an approximately 0.4 eV barrier that renders the S-S bond cleavage rate slow. However, for the excited Rydberg state, the intramolecular electron transfer has a much smaller barrier and is prompt.     

Structure, thermochemistry, and conformational analysis of peroxides ROOR and hydroperoxides ROOH (R = Me, But, CF3)

The equilibrium structures, total energies, and harmonic frequencies of peroxides ROOR and ROOH (R = Me, Bu^t, CF₃) were calculated using the perturbation theory (MP4//MP2 method) and density functional approach (B3LYP) in the 6-31G(d,p) basis set. The conformational flexibility of peroxides under rotation about the O-O bond was investigated. It was found that the stable conformation of a peroxide molecule is determined by superposition of the destabilizing effects (repulsion between the lone electron pairs, steric hindrances) and the interaction of the nonbonding orbitals of oxygen atoms with the antibonding orbitals of the adjacent polar bonds. The latter effect stabilizes the nonplanar structure of the peroxide molecule. The role of orbital interactions in manifestation of the d-effect (distortion of the tetrahedral configuration of the X₃CO fragment of peroxide molecule) was revealed. The vibrational spectra of peroxides were calculated and compared with the experimental data. The potential energy distribution over normal vibrations was analyzed. The enthalpies of formation and the bond strengths in the molecules of compounds examined were calculated in the framework of the isodesmic reaction approach.     

A 3D QSAR pharmacophore model and quantum chemical structure--activity analysis of chloroquine(CQ)-resistance reversal

Using CATALYST, a three-dimensional QSAR pharmacophore model for chloroquine(CQ)-resistance reversal was developed from a training set of 17 compounds. These included imipramine (1), desipramine (2), and 15 of their analogues (3-17), some of which fully reversed CQ-resistance, while others were without effect. The generated pharmacophore model indicates that two aromatic hydrophobic interaction sites on the tricyclic ring and a hydrogen bond acceptor (lipid) site at the side chain, preferably on a nitrogen atom, are necessary for potent activity. Stereoelectronic properties calculated by using AM1 semiempirical calculations were consistent with the model, particularly the electrostatic potential profiles characterized by a localized negative potential region by the side chain nitrogen atom and a large region covering the aromatic ring. The calculated data further revealed that aminoalkyl substitution at the N5-position of the heterocycle and a secondary or tertiary aliphatic aminoalkyl nitrogen atom with a two or three carbon bridge to the heteroaromatic nitrogen (N5) are required for potent "resistance reversal activity". Lowest energy conformers for 1-17 were determined and optimized to afford stereoelectronic properties such as molecular orbital energies, electrostatic potentials, atomic charges, proton affinities, octanol-water partition coefficients (log P), and structural parameters. For 1-17, fairly good correlation exists between resistance reversal activity and intrinsic basicity of the nitrogen atom at the tricyclic ring system, frontier orbital energies, and lipophilicity. Significantly, nine out of 11 of a group of structurally diverse CQ-resistance reversal agents mapped very well on the 3D QSAR pharmacophore model.     

A stable aminothioketyl radical in the gas phase

We report the first preparation of a stable aminothioketyl radical, CH(3)C(?)(SH)NHCH(3) (1), by fast electron transfer to protonated thioacetamide in the gas phase. The radical was characterized by neutralization-reionization mass spectrometry and ab initio calculations at high levels of theory. The unimolecular dissociations of 1 were elucidated with deuterium-labeled radicals CH(3)C(?)(SD)NHCH(3) (1a), CH(3)C(?)(SH)NDCH(3) (1b), CH(3)C(?)(SH)NHCD(3) (1c), and CD(3)C(?)(SH)NHCH(3) (1d). The main dissociations of 1 were a highly specific loss of the thiol H atom and a specific loss of the N-methyl group, which were competitive on the potential energy surface of the ground electronic state of the radical. RRKM calculations on the CCSD(T)/aug-cc-pVTZ potential energy surface indicated that the cleavage of the S-H bond in 1 dominated at low internal energies, E(int) < 232 kJ mol(-1). The cleavage of the N-CH(3) bond was calculated to prevail at higher internal energies. Loss of the thiol hydrogen atom can be further enhanced by dissociations originating from the B excited state of 1 when accessed by vertical electron transfer. Hydrogen atom addition to the thioamide sulfur atom is calculated to have an extremely low activation energy that may enable the thioamide group to function as a hydrogen atom trap in peptide radicals. The electronic properties and reactivity of the simple aminothioketyl radical reported here may be extrapolated and applied to elucidate the chemistry of thioxopeptide radicals and cation radicals of interest to protein structure studies.