Showing papers on "Transition state published in 1990"

Reaction path study of conformational transitions in flexible systems: Applications to peptides

Abstract: A new protocol to find minima and transition states in flexible systems is proposed. It is tested on alanine dipeptide (AD) with four minima and eight transition states and applied to a flexible molecule, isobutyryl–(ala)3–NH–methyl (IAN), the shortest peptide which can form a full helical turn. There were found 138 minima and 490 transition states for IAN. It is shown that the connectivity network between the minima is very dilute and composed of transitions localized on one or two neighboring amide units. Most of the transitions involve one or two dihedral flips. The reaction coordinate from an extended chain conformation to a helix follows a sequence of nonoverlapping rotations around bonds. The rotations along the reaction coordinates are such that the hard repulsions between different atoms are minimized but at the same time the hydrogen bonding and the electrostatic interactions are maximized. A melting‐like transition which is associated with the sudden opening of a large number of hopping channels is identified between minima at approximately 5 kcal/mol above the lowest energy minimum. The calculated minima and transition states are used to construct a master equation for the two molecules. The vibrational spectrum of the N–H stretch as a function of time and temperature is finally calculated. It is demonstrated that time‐dependent lineshape analysis can be a useful tool to investigate the properties of the large number of minima and the intervening transitions.

Single transition state in the transfer of a neutral phosphoryl group between phenoxide ion nucleophiles in aqueous solution

Abstract: The second-order rate constants (k ArO ) for reaction of substituted phenoxide ions with 4-nitrophenyl diphenyl phosphate obey a linear equation over a range of 18 substituents. The linear plot is consistent with a mechanism involving a single transition state or a two-step process with a very reactive intermediate with two almost identical transition states for its formation and breakdown; the value of the exponent (0.53) is also not consistent with a regular stepwise process with a discrete intermediate. The symmetrical reaction of 4-nitrophenolate ion with the 4-nitrophenyl ester is slightly imbalanced whereby bond formation does not keep up with bond fission in the transition states; the transition state, therefore, has some phosphorylium ion character. Transfer of the diethylphosphoryl group between weakly basic oxyanion nucleophiles is probably a concerted process with a transition state with more of the character of the pentacoordinate intermediate than it has in the corresponding diphenylphosphoryl group transfer

Ab initio conformational analysis of cyclohexane

Abstract: The inversion of cyclohexane has been studied by using ab initio molecular orbital theory. Six stationary points were found and characterized as minima or transition states. With a double-ζ basis augmented with a set of d-type polarization functions on each carbon, the geometries were optimized, and force constants were calculated. An MP-2 correlation correction was also evaluated with a much larger basis of triple-ζ plus polarization quality. The lowest energy structure is the chair conformation of D 3d symmetry. The other minimum is found to be the twist-boat structure of D 2 symmetry, which lies 6.9 kcal/mol higher in energy. A boat structure of C 2υ symmetry is a transition state, along a pseudorotational coordinate connecting two twist-boat structures

What Is the Effect of Variational Optimization of the Transition State on α-Deuterium Secondary Kinetic Isotope Effects? A Prototype: CD3H ⇆ CD3 + H2

Abstract: Variational Transition state theory calculations with semiclassical transmission coefficients have been carried out for a prototype case of α-deuterium secondary kinetic isotope effects (KIEs) in a reaction involving the transformation of an sp 3 carbon to sp 2 , in particular for the reactions of CH 4 and CD 3 H with H and D. We also study the KIE for the reverse direction and for the reactions of CH 4 and CD 3 H with D. We find that the variational transition states lead to significantly different nontunneling KIEs than the conventional ones, e.g., 1.22 vs. 1.07, and the inclusion of multidimensional tunneling effects increases the discrepancy even more. The origins of these variational and tunneling effects are examined in detail in terms of structures, vibrational frequencies, and the curvature of the reaction path. The conclusions have wide implications for the validity of conventional treatments of kinetic isotope effects

Chain length effects in the cleavage of aryl esters by cyclodextrins. Different transition states for m- and p-nitrophenyl alkanoates

Abstract: The kinetics of cleavage of m- and p-nitrophenyl esters (acetate, propanoate, butanoate, pentanoate, and hexanoate) in a basic aqueous phosphate buffer containing α- or β-cyclodextrin (α- or β-CD) have been measured. For these two series of esters the m-nitro derivatives undergo more efficient cleavage than their p-nitro isomers, indicating that the former react via a transition state in which the aryloxy moiety is included in the CD cavity, even though substrate binding probably occurs through the alkyl group. The present studies illustrate the usefulness of the pseudo constants pK TS (=-log K TS ), where K TS is the apparent dissociation constant of the transition state of the CD-mediated reaction into the transition state of the normal reaction and CD. The variation of these constants with structure can be a useful probe of mechanism, particularly with regard to the mode of binding of transition state of the CD-mediated reaction

A theoretical study on ketene-olefin cycloadditions. 1. Intermolecular reactions

Abstract: The cycloaddition reaction between ketenes and olefins, leading to cyclobutanones, has been theoretically studied by means of the semiempirical AM1 methodology. A representative set of 7 differently substituted ketenes and 3 olefins has been selected, and 50 transition states, corresponding to different ketene-olefin approach geometries, have been located and characterized. The reaction is seen to be concerted in all but in two cases, taking place through twisted transition states with small charge transfer from the olefin to the ketene. A reaction analysis by correlation of localized molecular orbitals shows that the reaction mechanism corresponds to the [π2 s +(π2 s +π2 s )] description, rather to the [π2 s +π2 a ] one. The regioselectivity and the stereoselectivity of the reaction are correctly predicted by the calculations and are analyzed in terms of electronic and steric effects of the substituents on the reacting ketene and olefin partners

Sequential clustering reactions of SiD+3 with SiD4 and SiH+3 with SiH4: Another case of arrested growth of hydrogenated silicon particles

Abstract: Sequential clustering reactions of SiD+3 with SiD4 and SiH+3 with SiH4 are observed in the ion cell of a Fourier transform mass spectrometer. Clustering occurs either by addition of SiD2 or SiH2 accompanied by loss of D2 or H2, or by the formation and stabilization of the bimolecular adducts. All of the clustering reactions are highly inefficient and lead to bottleneck structures at small silicon cluster sizes containing two to four silicon atoms. Rates are measured for both the addition and association products for each step of the reaction. Back reaction rates are monitored via silicon‐29 isotope exchange. Ab initio electronic structure calculations of the reaction pathways including intermediates, transition states and products have been performed by Raghavachari and are presented in his companion paper. The overall reaction mechanisms are similar for each reaction step. First an intermediate complex is formed between the ion and neutral which is strongly bound by a bridging deuterium or hydrogen atom....

A dynamic reaction coordinate approach to ab initio reaction pathways: Application to the 1,5 hexadiene Cope rearrangement

Abstract: A modified dynamic reaction coordinate algorithm for tracing reaction paths is implemented in the framework of ab initio molecular orbital calculations. This method requires fewer energy and gradient evaluations than the traditional intrinsic reaction coordinate methodology and produces reaction pathways of acceptable accuracy. The approach is applied to the 1,5 hexadiene Cope rearrangement for which we trace the pathways passing through the chair and boat transition states. Analysis of the lowest energy pathway indicates that the rearrangement is concerted and synchronous.

Prediction of nucleoside-carcinogen reactivity. Alkylation of adenine, cytosine, guanine, and thymine and their deoxynucleosides by alkanediazonium ions.

Abstract: MNDO semiempirical molecular orbital calculations for the SN2 alkylation of nucleic acid bases and deoxynucleosides by the methane-, ethane-, and propanediazonium ions are presented. An approximate correlation is demonstrated between the calculated relative activation enthalpies for attack at alternative base sites and the related experimental quantities for DNA modification by alkylnitrosoureas. The empirically observed shift from N- to O-alkylation with increasing complexity of the alkylating agent is reproduced by the calculations and rationalized by using an extension of a model worked out previously for the analogous reactions of simple nucleophiles. According to this model, the energetics of the related SN1 reactions, while not directly involved, have a profound influence on the SN2 transition-state geometries. For reactions in which the SN1 dissociation is unfavorable the forming bond to the incoming nucleophiles in the related SN2 transition state tends to be short and covalent interactions, which favor N-alkylation, play a significant role. When the SN1 reaction is more facile, the SN2 transition states are "looser" and the covalent interactions correspondingly smaller, leading to an overall shift away from N-alkylation. Consideration of the form of the electrostatic potential around the base, in conjunction with these ideas, provides a detailed explanation of the behavior of electrophiles toward the guanine N2-, 7-, and O6-positions. This model unifies much of the language already used in discussions of nucleic acid regiochemistry. At the same time it is consistent with the geometries and charge distributions in the transition states calculated for the gas-phase reaction processes.

Ring-opening reactions of dioxetene, oxetene, dithiete, and thiete

Abstract: A series of electrocyclic isomerizations related to the cyclobutene to butadiene reaction have been studied by ab initio theory. In addition to the cyclobutene isomerization, the ring-opening reactions of dioxetene, oxetene, dithiete, and thiete to cis-glyoxal, cis-acrolein, dithioglyoxal, and cis-thioacrolein have been examined. Structures and vibrational frequencies have been determined for reactants, transition states, and products with split-valence and split-valence plus polarization self-consistent field (SCF) methods. For the cyclobutene to butadiene, dioxetene to glyoxal, and oxetene to acrolein reactions, multiconfiguration SCF (MCSCF) geometries were optimized. The use of unrestricted Hartree-Fock natural orbitals (UHF-NO) to define the active space for complete active-space SCF (CASSCF) computations on the transition states was examined. MCSCF, configuration interaction (CISD), and Moller-Plesset perturbation theory (MP4SDTQ) methods were used to determine the activation barriers and reaction energies

Secondary 18O isotope effects as a tool for studying reactions of phosphate mono-, di-, and triesters.

Abstract: Secondary 18O isotope effects have been developed as a tool for determining transition state structures in enzymatic and nonenzymatic phosphoryl transfer reactions. 18O substitution in the nonbridge oxygens of a phosphoryl group makes the reaction go faster when the bond order is higher to these oxygens in the transition state than in the reactant, whereas the reaction goes slower if the bond order is less. The isotope effects are measured by the remote label method, using an isotope ratio mass spectrometer for analysis. The bond order to p-nitrophenolate ion when it is the leaving group is indicated by the secondary 15N isotope effect in the nitro group, with a value of 1.0028 representing nearly complete bond cleavage. It appears that the transition states for phosphoryl transfer have no more than one negative charge on the nonbridge oxygens, so that reactions of monoesters are dissociative, reactions of triesters are associative, and reactions of diesters are SN2 with half bond order to entering and le...

The quantum mechanical resonance energy of transition states: an indicator of transition state geometry and electronic structure

Abstract: This paper discusses the quantum mechanical resonance energy (B) of three-center transition states having three and four delocalized electrons, such as in atom transfer X-X-X and in polar group transfer reactions (X-A-X) − . It is shown that B is proportional to the energy difference between the HOMO and LUMO of the transition state, and any geometric variation that lowers the energy gap between these two orbitals of the transition state will also decrease its B property

Application of the GAPT population analysis to some organic molecules and transition structures

Abstract: Atomic charges in ozone, carbon monoxide, silylene, silaketene and dimethylsilaketene (for both the pyramidal minimum and the planar transition state), 2-methyl-2-silacyclopropanone, ethylenebromonium cation (open and bridged), (Z)-1,3-butadiene, 1,3-cyclopentadiene, cyclopropene, methylenecyclopropene, the transition state for the Diels-Alder reaction between 1,3-cyclopentadiene and cyclopropene, and (E,E,E,E,E)-1,3,5,7,9-decapentaene have been calculated within the recently introduced GAPT population analysis. Effects of different basis sets and electron correlation on the atomic charges have been examined. On the basis of these studies it is found that the GAPT population analysis should be recommended as a standard tool for analyzing the electronic structure of organic molecules and transition states.

Mechanistic aspects of biological redox reachtions involving NADH 2: a combined semiempirical and Ab-Initio study of hydride-ion transfer between the NADH analogue, 1-methyl-dibydronicotinamide, and folate and dihydrofolate analogue substates o f dihydrofolate reductase

Abstract: As part of a study of factors controlling biological redox reactions of nicotinamide cofactors [nicotinamide adenine dinucleotide (phosphate) NAD(P)H], we have investigated the effect on a model reaction of the conformational state (cis or trans) of the carboxamide side chain, using quantum chemical methods. The reaction is that for the enzyme dihydrofolate reductase between the NADPH analogue, 1-methyl-dihydronicotinamide, and the protonated forms of the folate and dihydrofolate substrate analogues, pyrazine and dihydropyrazine. Some calculations on pterin and dihydropterin substrate analogues were also carried out in order to gauge the effects of inter-ring coupling. The influence of carboxamide side-chain conformation of nicotinamide on the energetics of the hydride-ion transfer, and on the structures of the transition states and stable intermolecular-interaction complexes, are examined as a function of the orientation of approach of the reactants. These approach geometries include those corresponding to the observed binding of cofactor and either substrate or inhibitor in the enzyme active site. Reactant, product, reactants-complex, and transition-state geometries were optimized at the semiempirical AM1 level, while ab initio SCF/STO-3G and SCF/3-21G single-point calculations were carried out at the AM1 optimized geometries for all species, as well as full geometry optimizations for isolated reactants and products. The results show that reactants-complex and transition-state energies are lower for the trans conformer of dihydronicotinamide than for the cis conformer, due to more favorable H-bonding or electrostatic interactions with the protonated substrate. Also, consideration of the structural parameters, including reaction coordinate bond lengths, ring geometries, and charge distributions, indicate that the trans transition states are more product-like than those for the cis. For the (trans) approaches corresponding to the enzymic orientation for substrate, the intermolecular interaction for the folate reaction lacks the stabilizing influence of the formal H-bond which is present for the dihydrofolate reaction, and consequently the reactants-complex and transition state are less stable.

Ab initio studies on hydrogen‐bonded clusters: Structure and vibrational spectra of cyclic (HF)n complexes

Abstract: Equilibrium structures of cyclic (HF)n clusters with n = 3, 4, and 6, and vibrational spectra of cyclic (HF)3 and (HF)4 were investigated with the aid of ab initio methods including electron correlation at a size-extensive level. Computed ground state properties such as equilibrium structures, stabilization energies, harmonic vibrational frequencies, and infrared intensities are compared with the corresponding quantities of HF monomer and dimer. Trends in the modifications of monomer properties as induced by cluster formation are monitored. Results for the structure and energetics of cyclic Dnh transition states of (HF)n with n = 2, 3, 4, and 6 are also reported.

Reactivity of biologically important reduced pyridines

Abstract: The interaction of 1-methyl-1,-dihydronicotinamide and its corresponding pyridinium salt was examined using the AM1and MNDO molecular orbital approximations. Four initial approach vectors leading to various possible transition states were considered. The starting geometry which lead to the lowest energy transition state was one in which the pyridine rings were initially endo with respect to one another and in which the carboxamide groups were juxtapositioned. In the optimized geometry, the amide groups had separated minimizing steric interaction. This structure could not freely rotate around the axis of the transferring hydride species although it could be distorted along this axis with only modest energetic cost. The approach of the two heterocycles from 100 A to the transition state was subsequently examined. A charge-induced dipole complex was observed on the reaction coordinate between 4 A and 2 A intermolecular separation. This complex appeared to be extremely important in positioning the interacting molecules. Closer approach led to the transition state in which the hydride component was transferred in a linear fashion. No low-energy charge-transfer complexes were encountered along the reaction coordinate.

The use of crystal data together with other experimental and computational results to discuss structure-reactivity and activity relationships

Abstract: The understanding of chemical reactivity and biological activity requires knowledge of the three-dimensional structure of molecules and information about their conformational flexibility. Whereas crystallographic diffraction methods make ground-state structures easily available, the study of dynamic processes such as molecular transformations, intermediates, and transition states during chemical reactions; conformational interconversions; or drug-receptor interactions demand the combination of several complementary techniques. Because each of these methods has its inherent limitations, the results obtained from different sources must be checked. In the present study crystallographic data are used together with the results of spectroscopic, kinetic, and computational techniques (1) to discuss conformational flexibility and preferences of Ph-X-Ph [X=CH2, C(CR n )2 (n=2, 3), C=0, NH, NR (R=C, N), O, S, SO2], R2N+ (n-Pr)2 derivatives and caprylolactam, (2) to describe nucleophilic addition of N toward a carbonyl group during a ring-closure reaction in heterocylic systems, (3) to investigate SN2 substitution at silicon, and (4) to visualize topochemical interconversion pathways in pentacoordinate complexes.

Ab initio study of substituent effect on the addition of hydrogen fluoride to fluoroethylenes

Abstract: An ab initio 3-21G study of the direct addition of HF to C2HnF(4–n), with n = 0 to 4, has been performed to investigate the effect of the substituent on the reaction. Geometry optimization of all charge-transfer complexes and transition states has been done. Standard analysis of activation energies of addition reactions, vibrational and thermodynamical analysis, as well as Morokuma energy decomposition, BSSE correction, PMO analysis, and Pauling bond orders were used to explain the results. A subset of the reactions, including that of C2H4 as reference one and the two most favorable cases, was also studied at the MP2/6–31G(d,p)//HF/6–31G(d,p) level. The barriers so obtained are in agreement with the indirectly found from experimental data. It was found that the effect of the substituent is not monotonic for the additions. Decomposition of the interaction energy is shown to be adequate to explain this nonmonotonic behavior. The implications for laser chemistry of the addition of hydrogen halides to fluorosubstituted olefins is briefly discussed.

The mass weighting problem of potential energy surfaces for chemical reactions: dissociation and isomerisation pathways of HCN

Abstract: The mass-weighting problem is discussed in the context of the reaction pathways of a chemical rearrangement. Some simple differential geometrical relations are used to connect different coordinate systems and achieve an independent definition of a reaction path from the coordinate system. In order to describe the procedure in more detail, it is applied to the molecule hydrogen cyanide (HCN) and its different reaction paths. The action of mass weighting on these paths is illustrated.

An Ab Initio Molecular Orbital Study on the Ene Reaction of Methyl Acrylate with Propene

Abstract: 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...

Fundamental aspects of chemical kinetics in condensed phases

Abstract: Solvents can exert strong effects on chemical reaction rates. The interaction of solvent with reactant species causes shifts in transition states, replacing the gas phase saddle point with a distribution of saddle points differing in height, extent of asymmetry, curvatures, etc. The effect of such a distribution on measured reaction rates can be assessed with an extension of the Stillinger-Weber inherent structure theory. This theory uses a mass-weighted descent mapping to partition the multidimensional configuration space into distinct potential energy “basins”; in the present work these are classified by the numbers of reactant and product species present at the minima. Chemical transition states are flanked by pairs of “gateway” basins. We have implemented this formalism numerically and located the actual chemical transition states for a molecular dynamics model of the exchange reaction F + F2 ⇌ F2 + F in liquid argon. In the dense solution, the frequency of trajectory recrossings through the transition state exceeds that in the gas phase reaction. Most of this difference stems from the changes in geometry of reactants at the distribution of reactive saddle points.