An ab initio study of amide proton shift tensor dependence on local protein structure.

Ab initio shielding tensor calculations were carried out on residues in human ubiquitin. Reported experimental data on isotropic and anisotropic components of the amide proton chemical shifts were used as benchmarks to test the validity of the chosen basis sets as well as methods in structure optimization and shielding calculations. The best agreement with the experimental values was observed when the 6-311**G and 6-311++G(2d,2p) basis sets were used to optimize the structure and to calculate the shielding tensor, respectively. The same method was employed in subsequent model calculations to characterize the dependence of amide proton shielding to the local structure. Both the isotropic and the anisotropic components of the symmetric tensor were found to depend very strongly on the hydrogen bond length. A weaker dependence can also be observed for the hydrogen bond angle. Antisymmetric tensor elements were found to be relatively small. This study permits separation of various local structure contributions to the amide proton shielding tensor that complements scarce experimental data.     

AB initio calculations on the hydration energies of Br− Ion

The energies of hydrated Br^? ion for coordination numbers up to 4 have been calculated with an ab inito MO method. The most favorable orientation is the ion—dipole one, in contrast to the H-bonded orientation for Cl^?(H₂O) and F^?(H₂O). The hydration energies calculated in this study are in fair agreement with those obtained by Arshadi.     

Ab initio studies of the intramolecular amide hydrolysis in N-methylmaleamic acids

The intramolecular amide hydrolysis reactions of N-methylmaleamic acids (NMMA) are studied at the MP2/6-31G**//RHF/4-31G level of theory as model reactions of peptide bond cleavage by a proteolytic enzyme. In contrast to the previously reported results for a bimolecular reaction model of peptide hydrolysis, the unimolecular reactions studied here proceed via the concerted pathway in which the C–O bond formation and the release of methylamine occur simultaneously in preference to the stepwise one. The determination of an intrinsic reaction coordinate shows that the reaction is facilitated by the intramolecular proton transfer from the undissociated carboxyl group to the nitrogen of the leaving amine group. Mainly because of the increase in activation energy, methyl substitution at the 2-position retards the hydrolysis reaction rate by a factor of 14 compared to the reaction of the unsubstituted molecule. In contrast, additional methyl substitution at 3-position leads to 35-fold increase in the reaction rate. These variations of reactivity are caused by the charge redistributions in the amide group induced by methyl substitutions and the resulting changes in electrophilicity of the aminocarbonyl carbon.     

An ab initio and DFT study on the hydrolysis of carbonyl dichloride

Hydrolysis of carbonyl dichloride or phosgene (Cl₂CO) in gas phase has been investigated at Hartree–Fock, density functional and ab initio levels of theory. The effects of basis sets on the energetics of the reaction have also been explored. Calculations reveal that initially carbonyl dichloride and water form a weak complex and this complex can react further in two ways. In Path 1, water adds on to carbonyl dichloride across carbonyl bond in a concerted fashion to give dichloromethane diol, and this diol decomposes to form chloro formic acid by syn-1,2-elimination of HCl and forms CO₂ and HCl as final products. Path 2 is the concerted addition of water across carbon chlorine bond and elimination of HCl in a single step leading to the formation of chloro formic acid directly. This second path that skips the formation of dichloromethane diol is observed to be very low lying and hence is kinetically favored. Addition of second water molecule to the reacting system is found to catalyze the reaction by stabilizing the complex, intermediate and transition states and reduces the activation energy to 24.6 kcal mol⁻¹ compared to 29.9 kcal mol⁻¹ for a single water molecule.     

Modeling dependence of the strength of agglomerates on their basicity

An attempt was performed to clarify and summarize mathematically an extreme dependence strength-basicity of agglomerate based on polymorphism of Ca₂SiO₄. Two main indicators underlaid the sinter production: a mechanical strength and specific performance of a sinter plant, which can be expressed by yield of a certain size fractions after physical stress and by linear sintering rate, respectively.     

AB initio calculation of vertical transition energies of the C2H2 molecule

Various ab initio SCF and Cl treatments are reported for the acetylene molecule in ground and excited states at its fixed linear equilibrium geometry. The results speak in favor of the former analysis of the vacuum UV absorption spectra of C₂H₂ given by Wilkinson according to which above the X?C state an allowed transition to a linear upper state (X?D) and two allowed transitions with broad bands (X?E and X?F) to non-linear upper states are present. The calculated order and spacing of the excited states does not support the new analysis given by Jungen according to which only one allowed transition (X?F) and a forbidden one to a linear upper state (X?D) should appear between 1250 and 1360 A.     

Valence photoelectron spectrum of CoO. Ab initio calculations of energies and relative intensities within a limited CI framework

The valence spectrum of CoO has been calculated using the CoO₆^10? cluster, stabilized by an electrostatic field, as a model of bulk CoO. The wave functions were generated using basis sets of better than double-zeta quality. SCF wave functions were obtained for the ground state and for the first ionized state of the cluster. Limited CI calculations were performed using these orbital sets. The lowest states of the ion correspond to the main lines in the spectrum, while higher states can give rise to high-energy satellites to the main lines. The relative intensities of these satellites were estimated in the case of high-energy incident photons.     

An AB initio molecular orbital study of the PF2 radical

Gaussian orbital calculation of the ESR coupling constants in the PF₂ radical are presented, in excellent agreement with experiment.     

An ab initio close-coupling calculation of the lower vibrational energies of the HCl dimer

We have previously determined an analytical ab initio six-dimensional potential energy surface for the HCl dimer, and in the present paper we use this potential, with the HCl bond lengths held fixed, in a full (four-dimensional) close-coupling calculation to determine the energies of the lowest 24 vibrational states. These vibrational states involve the intermolecular stretch ν₄, the trans-bend tunneling vibration ν₅, and the torsion ν₆. The highest of the 24 levels is the (ν₄ν₅ν₆)=(111) state, for which we calculate an energy of 200 cm⁻¹ above the (000) state. As well as determining tunneling energies up to 5ν₅=183 cm⁻¹, we determine ν₄=49 cm⁻¹, 2ν₄=93 cm⁻¹, 3ν₄=134 cm⁻¹, 4ν₄=172 cm⁻¹, ν₆=137 cm⁻¹ and ν₄+ν₆=178 cm⁻¹, together with tunneling energies in all these states. Making allowance for the HCl stretching zero-point energy we determine the dissociation energy D₀ as 390 cm⁻¹ on this analytical surface. We determine that below 300 cm⁻¹ there are 72 vibrational (J=K=0) states, and below dissociation there are 162 vibrational (J=K=0) states, for this potential surface.     

Ab initio GB study of chemical intermediates in solution; Ethylenesulfonium ion in hydrolysis of 2-chloroethyl methyl sulfide

Ab initio MO theory including solvent effects has been applied to the structure and reactivity of methyl ethylenesulfonium ion, 1 , in aqueous solution as a model of the three-membered cyclic sulfonium intermediate expected in the toxic action of sulfur mustard. The 6-31 + G* geometry optimization of the cyclic sulfonium ion 1 suggested that the ring size of 1 is expanded slightly by solvation. The contour lines map of the interaction energy between 1 and Cl⁻ has a very shallow and wide well at 5–6 Å distance from 1 . This is the solvent-separated ion pair, and the contact ion pair was not found between 1 and Cl⁻. The calculated energy diagrams for the S_N2-type reactions of 1 with Cl⁻, H₂O, and OH⁻ that give ring-opened compounds indicated the following: (1) The energy of the 1 + Cl⁻ system is similar to that of chloroethyl methyl sulfide (CEMS, 2 ), and the interconversion between 1 + Cl⁻ and 2 occurs easily in aqueous solution. The 3-21 + G(*) and 6-31 + G* activation energies for the 2 → 1 + Cl⁻ reaction, 20–22 kcal/mol, agree well with the experimental enthalpy of activation for the hydrolysis of 2 . (2) The reaction of 1 with OH⁻ gives a very stable hydroxyl compound, 4 , and no transition state was found. (3) The reaction of 1 with H₂O gives an unstable addition product that is expected to be converted to 4 with the assistance of another H₂O molecule. This mechanism is consistent with that proposed by Bartlett and Swain in their pioneering work on the hydrolysis of sulfur mustard. © 1998 John Wiley & Sons, Inc. Heteroatom Chem 9:503–510, 1998     

A comparison of the relative energies of isomeric intermediates formed in electrophilic,radical, and nucleophilic aromatic substitution reactions

The relative energetics of isomeric σ-complex intermediates formed in electrophilic, free radical, and nucleophilic attack of Cl, H, and Me on PhCl and PhMe are compared for all positions: o, m, p, and ipso. The results are presented as ΔH, computed by the MINDO/3 method, for the appropriate isodesmic reaction with benzene. For the chlorobenzene intermediates, there is a marked increase in the relative preference for the ipso-position as the reactions change from electrophilic to free radical to nucleophilic. For toluene intermediates, the order of stability-p > o > m > ipso-is seen in all reactions except for one case, free radical methylation. In general, the free radical intermediates show the smallest range of energy differences. Comparison of predictions from these calculations with experimental results (largely partial rate factors and product ratios) shows some qualitative agreement.     

AB initio calculations on the equilibruim geometry and rotation barriers in biphenyl

The geometry of the biphenyl molecule has been studied with the MO LCAO method using a gausian basis set of “double zeta” quality. For various values of the twist angle between the phenyl ring planes the positions of the hydrogen atoms in the 2-position and the distance between the two rings have been simultaneously optimized. The lowest energy has been obtained for a non-planar conformation having a twist angle of 32°. The rotation barriers are 1.2 and 4.5 kcal/mol for the planar perpendicular cases, respectively.     

Effect of cyclodextrin on the intramolecular catalysis of amide hydrolysis

The hydrolysis reaction of phthalamic acids (HOOCArCONHR, R = p-NO(2)Ph 1a, Ph 1b, adamantyl 1c) and N-phenyl maleamic acid 2b was studied in the presence of hydroxypropyl-beta-cyclodextrin (HPCD) in acid solution. The reactions of 1a and 1b were studied also in the presence of beta-cyclodextrin (beta-CD). All the compounds formed inclusion complexes with HPCD, and the association constant was determined from the change in absorption of the substrate when the host is added in the case of 1a (90 M(-)(1)) and 2b (49 M(-)(1)). For 1c ( 4 x 10(4) M(-)(1)) a competition method was used, and for 1b the association equilibrium constant was obtained from the kinetic data (37 M(-)(1)) because it is too reactive for the spectrophotometric method. Both cyclodextrins strongly inhibited the reactions, and analysis of the kinetic data for HPCD indicated that the reactions of complexed 1a, 1b, and 2b are at least 10-30 times slower than in the bulk solution whereas 1c reacts only 4.6 times slower when it is complexed. The inhibition is attributed to changes in the geometry of the substrate due to interaction of the carboxylic group and/or the amide with the OH at the rim of the cyclodextrin. The differences in the relative effect observed for 1c are attributed to the formation of a tighter complex with this substrate.     

An Ab initio study on the conformations of protonated,neutral, and deprotonated amidine

Ab initio SCF molecular orbital calculations have been performed to ascertain the conformational preferences of protonated, neutral, and deprotonated amidine [HC(?NH)NH₂], using the 3-21G split valence basis set. The states of eight stable species, eight transition states, and four higher-order saddle points have been determined by complete geometry optimization utilizing analytic energy gradient techniques. Protonation at the amidine ?NH is preferred over the –NH₂ site by 37.1 kcal/mol. Neutral amidine has rotational barriers of 9.6 and 11.7 kcal/mol for the HN?CN cis and trans isomers, respectively, while all the stable HC(NH₂)₂⁺ and HC(NH)₂^? species possess torsional barriers larger than 23 kcal/mol. There is, however, essentially free C—N single-bond rotation in HC(?NH)NH₃⁺, the calculated barriers being 0.7 and 1.8 kcal/mol for the cis and trans HN?CN isomers, respectively.     

An ab initio study of the A Ac1 hydrolysis mechanism of formamide

Ab initio calculations have been used to examine the reaction profile for the A _wc1 hydrolysis mechanism for formamide, giving a value of 67.3 kcal/mole for H . Comparisons between computed and experimental proton affinities are used to assess the reliability of the calculations. Orbital energies are reported for formamide, N-protonated and O-protonated formamide, carbon monoxide and the formyl cation.     

AB initio calculation of the spin dipole-dipole interaction in ground-state triplets

Ab initio results are presented for the spin dipole-dipole interaction in the ground-state linear triplet radicals NCN, CNN and CCO. The relative contributions from the first-order spin dipole-dipole interaction and the second-order spin-orbit interaction, to the observed spin coupling constant in these systems, are discussed.