Einar Uggerud

Integration of the classical equations of motion on ab initio molecular potential energy surfaces using gradients and Hessians: application to translational energy release upon fragmentation

Abstract A new method for calculating classical trajectories on molecular ab initio potential energy surfaces is presented. The equations of motion are integrated on a sequence of model surfaces constructed from analytically calculated molecular gradients and Hessians. The method avoids the explicit calculation of the total surface and is therefore applicable whenever the gradient and Hessian can be calculated. The method is applied to the unimolecular fragmentations of H 3 and CH 2 OH + , yielding the translational energy released upon separation of the products.

Gas phase nucleophilic substitution

Abstract The literature on gas phase nucleophilic substitution reactions at aliphatic carbon has been reviewed. The emphasis has been on journal articles published in the period 1990–2001. The present review outlines our current understanding of concepts such as potential energy surfaces, structure–energy relationships, microsolvation, and dynamical and mechanistic details based on both experimental and theoretical evidence. The accuracy of various theoretical schemes for calculating potential energy surfaces has been assessed. A critical account on mechanistic concepts used in the literature is given.

THE GAS-PHASE FORMATION OF METHYL FORMATE IN HOT MOLECULAR CORES

Methyl formate, HCOOCH3, is a well-known interstellar molecule prominent in the spectra of hot molecular cores. The current view of its formation is that it occurs in the gas phase from precursor methanol, which is synthesized on the surfaces of grain mantles during a previous colder era and evaporates while temperatures increase during the process of high-mass star formation. The specific reaction sequence thought to form methyl formate, the ion-molecule reaction between protonated methanol and formaldehyde followed by dissociative recombination of the protonated ion [HCO(H)OCH3] + , has not been studied in detail in the laboratory. We present here the results of both a quantum chemical study of the ion-molecule reaction between [CH3OH2] + and H2CO as well as new experimental work on the system. In addition, we report theoretical and experimental studies for a variety of other possible gas-phase reactions leading to ion precursors of methyl formate. The studied chemical processes leading to methyl formate are included in a chemical model of hot cores. Our results show that none of these gas-phase processes produces enough methyl formate to explain its observed abundance. Subject headingg ISM: molecules — molecular data — molecular processes — radio lines: ISM

Single-Molecule Force Spectroscopy Measurements of Bond Elongation during a Bimolecular Reaction

It is experimentally challenging to directly obtain structural information of the transition state (TS), the high-energy bottleneck en route from reactants to products, for solution-phase reactions. Here, we use single-molecule experiments as well as high-level quantum chemical calculations to probe the TS of disulfide bond reduction, a bimolecular nucleophilic substitution (S N2) reaction. We use an atomic force microscope in force-clamp mode to apply mechanical forces to a protein disulfide bond and obtain force-dependent rate constants of the disulfide bond reduction initiated by a variety of nucleophiles. We measure distances to the TS or bond elongation (Delta x), along a 1-D reaction coordinate imposed by mechanical force, of 0.31 +/- 0.05 and 0.44 +/- 0.03 A for thiol-initiated and phosphine-initiated disulfide bond reductions, respectively. These results are in agreement with quantum chemical calculations, which show that the disulfide bond at the TS is longer in phosphine-initiated reduction than in thiol-initiated reduction. We also investigate the effect of solvent environment on the TS geometry by incorporating glycerol into the aqueous solution. In this case, the Delta x value for the phosphine-initiated reduction is decreased to 0.28 +/- 0.04 A whereas it remains unchanged for thiol-initiated reduction, providing a direct test of theoretical calculations of the role of solvent molecules in the reduction TS of an S N2 reaction. These results demonstrate that single-molecule force spectroscopy represents a novel experimental tool to study mechanochemistry and directly probe the sub-ångström changes in TS structure of solution-phase reactions. Furthermore, this single-molecule method opens new doors to gain molecular level understanding of chemical reactivity when combined with quantum chemical calculations.

Rate-Determining Factors in Nucleophilic Aromatic Substitution Reactions

Quantum chemical calculations (OPBE/6-311++G(d,p)) have been performed to uncover the electronic factors that govern reactivity in the prototypical S(N)Ar reaction. It was found that intrinsic nucleophilicity--expressed as the critical energy (the energy required for forming the Meisenheimer structure Ph(X)(2)(-)) in the identity substitution reaction X(-) + PhX --> X(-) + PhX (Ph = phenyl)--shows the following approximate trend: NH(2)(-) approximately OH(-) approximately F(-) >> PH(2)(-) approximately SH(-) approximately Cl(-) > AsH(2)(-) approximately SeH(-) approximately Br(-). The periodic trends are discussed in terms of molecular properties (proton affinity of X(-) expressing Lewis basicity of the nucleophile and C(1s) orbital energy expressing Lewis acidity of the substrate) based on a dative bonding model. Furthermore, the stepwise progress of the reactions and the critical structures are analyzed applying energy decomposition analysis. Increased stability, and thereby increased intrinsic nucleophilicity, correlates with decreasing aromatic character of the Meisenheimer structure. This apparent contradiction is explained in consistency with the other observations using the same model.

The Interplay between Steric and Electronic Effects in SN2 Reactions

Myths of steric hindrance: In contrast with current opinion, energy decomposition analysis shows that the presence of bulky substituents at carbon leads to the release of steric repulsion in the transition state shown in the graphic. It is rather the weakening of the electrostatic attraction, and in particular the loss of attractive orbital interactions, that are responsible for the activation barrier. Quantum chemical calculations for S(N)2 reactions of H(3)EX/X(-) systems, in which E=C or Si and X=F or Cl, are reported. In the case of the carbon system we also report on bulkier species in which the hydrogen atoms are substituted by methyl groups. It is shown how the variation in the individual energy terms of the Morokuma/Ziegler energy decomposition analysis (EDA) scheme along the reaction coordinate from reactants to products provides valuable insight into the essential changes that occur in the bond-breaking/bond-forming process during S(N)2 reactions. The EDA results for the prototypical S(N)2 reaction of the systems [X...R(3)E...X](-), in which the interacting fragments are [X...X](2-) and [R(3)E](+), have given rise to a new interpretation of the factors governing the reaction course. The EDA results for the carbon system (E=C) show that there is less steric repulsion and stronger electrostatic attraction in the transition structure than in the precursor complex and that the energy increase comes mainly from weaker orbital interactions. The larger barriers for systems in which R(3) is bulkier also do not arise from increased steric repulsion, which is actually released in the transition structure. It is rather the weakening of the electrostatic attraction, and in particular the loss of attractive orbital interactions, that are responsible for the activation barrier. The D(3h) energy minima of the silicon homologues [XH(3)SiX](-) is driven by the large increase in the electrostatic attractions and also of stronger orbital interactions, while the steric interactions is destabilizing.

Models of fragmentations induced by electron attachment to protonated peptides

Invoking a number of theoretical levels ranging from HF/STO-3G to CCSD(T)/aug-cc-pVQZ, we have made a detailed survey of six potential energy surfaces (NH4+, NH4•, [CH3CONHCH3]H+, [CH3CONHCH3]H•, [HCONHCH2CONH2]H+ and [HCONHCH2CONH2]H•). In conjunction with this, ab inito direct dynamics calculations have been conducted, tracing out several hundred reaction trajectories to reveal details of the electron-capture dissociation mechanism. The model calculations suggest the possibility of a bimodal pattern where some of the radicals, formed upon recombination, dissociate almost directly within one picosecond, the remaining radicals being subject to complete energy redistribution with a subsequent dissociation occurring at the microsecond timescale. Both processes give rise to c and z backbone fragments, resulting from cleavage of N?Cα bonds of the peptide chain.

Translational energy release: Experiment and theory. H2 elimination reactions of small gas phase ions, and correspondence to HH bond activation

All unimolecular decompositions are accompanied by a specific translational energy release. Translational energy release distributions can be precisely measured with a magnetic sector mass spectrometer. The experimental methods used for this purpose are described. The precise amount of translational energy released in the common centre of mass formed in a fragmentation reaction is a direct outcome of the detailed reaction dynamics of the system. It is described how recent development in reaction trajectory calculations with ab initio quantum chemical potential energy functions can be used to calculate translational energy release. The shape of a potential energy surface, and in particular the barrier height, are important for how much energy is released. In this review a much studied reaction type, H2 eliminations is reviewed. The reviewer has carefully examined the individual reactions in order to reveal the electronic factors that determine the shape of the potential energy profile. It turns out that frontier orbital theory provides a simple and solid theoretical framework. ©1999 John Wiley & Sons, Inc. Mass Spec Rev 18: 285–308, 1999

Reactions of platinum clusters Ptn±, n = 1–21, with CH4: to react or not to react

The relative reactivity of any given neutral platinum cluster falls in-between that of the corresponding anion and cation.

Gas phase reactivity of small cationic cobalt clusters towards methanol

Abstract The gas phase reactivity of small cationic cobalt clusters, Co n + (n=1–12) , towards methanol has been investigated using Fourier transform ion cyclotron resonance mass spectrometry. Sequential addition of methanol molecules to the clusters was observed to be the dominating process, with the exception of Co4+ and Co5+, for which dehydrogenation of methanol was the dominating initial reaction step. Isotopic labelling studies with CD3OH showed that the dehydrogenation is a 1,1-elimination reaction involving the methyl group. Loss of a cobalt atom upon methanol addition was also observed to be a facile process, being most pronounced for Co2+, Co3+ and Co6+.