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Jack Simons

Publications and source records attributed to Jack Simons.

18 recordsLinked to original sources
PubMed2007

Electron binding capabilities of some silylenes having small singlet-triplet splittings or triplet ground states.

Several silyl and alkaline metal substituted silylenes have been investigated using the CAS-ACPF method in conjunction with the aug-cc-pVTZ basis sets. Silylsilylene and disilylsilylene are found to have singlet ground states with DeltaEST(-) values of 0.676 and 0.319 eV, respectively. The adiabatic ground state electron affinities are found to be 1.572 and 2.361 eV for HSiSiH(3) and Si(SiH(3))(2). respectively. Both silylenes possesses a stable 2A1 excited negative ion state, with respective adiabatic EA values of 0.037 and 1.000 eV. In contrast, all silylenes with at least one akaline metal substituent exhibit triplet neutral ground states. The metalated silylenes HSiLi, HSiNa, LiSiSiH(3), NaSiLi, SiLi(2), and SiNa(2) have adiabatic ground state EAs somewhat below 1 eV, but each of these negatively charged system possesses up to three bound excited negative ion states, some of which are dipole-bound states.

Journal Article↗
PubMed2006

Catalytic hydrodeoxygenation of methyl-substituted phenols: correlations of kinetic parameters with molecular properties.

The hydrodeoxygenation of methyl-substituted phenols was carried out in a flow microreactor at 300 degrees C and 2.85 MPa hydrogen pressure over a sulfided CoMo/Al(2)O(3) catalyst. The primary reaction products were methyl-substituted benzene, cyclohexene, cyclohexane, and H(2)O. Analysis of the results suggests that two independent reaction paths are operative, one leading to aromatics and the other to partially or completely hydrogenated cyclohexanes. The reaction data were analyzed using Langmuir-Hinshelwood kinetics to extract the values of the reactant-to-catalyst adsorption constant and of the rate constants characterizing the two reaction paths. The adsorption constant was found to be the same for both reactions, suggesting that a single catalytic site center is operative in both reactions. Ab initio electronic structure calculations were used to evaluate the electrostatic potentials and valence orbital ionization potentials for all of the substituted phenol reactants. Correlations were observed between (a) the adsorption constant and the two reaction rate constants measured for various methyl-substitutions and (b) certain moments of the electrostatic potentials and certain orbitals' ionization potentials of the isolated phenol molecules. On the basis of these correlations to intrinsic reactant-molecule properties, a reaction mechanism is proposed for each pathway, and it is suggested that the dependencies of adsorption and reaction rates upon methyl-group substitution are a result of the substituents' effects on the electrostatic potential and orbitals rather than geometric (steric) effects.

Journal Article↗
PubMed2006

Solid-state NMR spectra and long intradimer bonds in the pi-[TCNE]22- dianion.

The principal (13)C chemical-shift values for the pi-[TCNE](2)(2-) dimer anion within an array of counterions have been measured to understand better the electronic structure of these atypical chemical species in several related TCNE-based structures. The structure of pi-[TCNE](2)(2-) is unusual as it contains two very long C-C bond lengths (ca. 2.9 Angstroms) between the two monomeric units and has been found to exist as a singlet state, suggestive of a (1)A(1g) (b(2u)(2)b(1g)(0)) electronic configuration. A systematic study of several oxidation states of [TCNE](n) (n = 0, 1-, 2-) was conducted to determine how the NMR chemical-shift tensor values change as a function of electronic structure and to understand the interactions that lead to spin-pairing of the monomer units. The density functional theory (DFT) calculated nuclear shielding tensors are correlated with the experimentally determined principal chemical-shift values. Such theoretical methods provide information on the tensor magnitudes and orientations of their principal tensor components with respect to the molecular frame. Both theoretical and experimental ethylenic chemical-shielding tensors reveal high sensitivity in the component, delta(perpendicular), lying in the monomer molecular plane and perpendicular to the pi-electron plane. This largest shift dependence on charge density is observed to be about -111 ppm/e(-) for delta(perpendicular). The component in the molecular plane but parallel to the central C=C bond, delta(parallel), exhibits a sensitivity of approximately -43 ppm/e(-). However, the out-of-plane component delta'(perpendicular) shows a minimal dependence of -2.6 ppm/e(-) on the oxidation state (n) of [TCNE](n). These relative values support the claim that it is changes within the ethylenic pi-electrons and not the sigma-electrons that best account for the dramatic variations in bonding and shift tensors in this series of compounds. Concerning the intraion bonding, relatively weak Wiberg bond orders between the two monomeric components of the dimer correlate with the long bonds linking the two [TCNE(*)](-) monomers. The chemical-shift tensors for the cyano group, compared to the ethylene shifts, exhibit a reduced sensitivity on the TCNE oxidation state. The experimental principal chemical-shift components agree (within typical errors) with the calculated quantum mechanical shieldings used to correlate the bonding. The embedded ion model (EIM) was used to investigate the typically large electrostatic lattice potential in these ionic materials. Chemical-shielding principal values calculated with the EIM model differ from experiment by +/-3.82 ppm on average, whereas in the absence of an electrostatic field model, the experimental and theoretical results agree by +/-4.42 ppm, which is only a modest increase in error considering the overall ionic magnitudes associated with the tensor variations. Apparently, the effects of the sizable long-range electrostatic fields cancel when the shifts are computed because of lattice symmetry.

Anions↗
PubMed2006

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.

Journal Article↗
PubMed2006

Simulating electron transfer attachment to a positively charged model peptide.

Ab initio electronic structure methods, including stabilization method tools for handling electronically metastable states, are used to treat a model system designed to probe the electron-transfer event characterizing electron-transfer dissociation (ETD) mass spectroscopic studies of peptides. The model system consists of a cation H(3)C-(C=O)NH-CH(2)-CH(2)-NH(3)(+), containing a protonated amine site and an amide site, that undergoes collisions with a CH(3)(-) anion. Cross-sections for electron transfer from CH(3)(-) to the protonated amine site are shown to exceed those for transfer to the Coulomb-stabilized amide site by 2 orders of magnitude. Moreover, it is shown that the fates of the amine-attached and amide-attached species are similar in that both eventually lead to the same carbon-centered radical species H(3)C-((*)C-OH)NH-CH(2)-CH(2)-NH(2), although the reaction pathways by which the two species produce this radical are somewhat different. The implications for understanding peptide fragmentation patterns under ETD conditions are also discussed in light of this work's findings.

Amides↗
PubMed2006

Transition-state energy and geometry, exothermicity, and van der Waals wells on the F + H2 --> FH + H ground-state surface calculated at the r12-ACPF-2 level.

Explicitly correlated averaged coupled-pair functional methods have been used to compute the ground-state Born-Oppenheimer potential energy surface for the F + HH' --> FH + H' reaction at the F + HH' and FH + H' asymptotes, the F...HH', and FH...H van der Waals wells, the reaction transition state, and at points along the intrinsic reaction coordinate connecting all of these stationary points. To these energies, corrections for spin-orbit coupling and scalar relativistic effects were added to produce total electronic energies whose accuracy is demonstrated to be very high (e.g., 0.1 kcal mol(-1)). The final data are used to refine the two-body parts of the currently best three-dimensional potential energy surface for this reaction, to predict several spectroscopic parameters of the species involved, and to offer accurate estimates of the title reaction's exothermicity (32.0 kcal mol(-1)) and activation barrier (1.8 kcal mol(-1)) as well as the geometry of the transition state.

Journal Article↗
PubMed2006

How do low-energy (0.1-2 eV) electrons cause DNA-strand breaks?

We overview our recent theoretical predictions and the innovative experimental findings that inspired us concerning the mechanisms by which very low-energy (0.1-2 eV) free electrons attach to DNA and cause strong (ca. 4 eV) covalent bonds to break causing so-called single-strand breaks. Our primary conclusions are that (i) attachment of electrons in the above energy range to base pi* orbitals is more likely than attachment elsewhere and (ii) attachment to base pi* orbitals most likely results in cleavage of sugar-phosphate C-O sigma bonds. Later experimental findings that confirmed our predictions about the nature of the electron attachment event and about which bonds break when strand breaks form are also discussed. The proposed mechanism of strand break formation by low-energy electrons involves an interesting through-bond electron-transfer process.

DNA↗
PubMed2005

Backbone and side-chain cleavages in electron detachment dissociation (EDD).

Ab-initio electronic structure methods are used to explore potential energy profiles pertinent to the fragmentations of gas-phase radicals thought to be formed in the new negative-ion mode EDD mass spectroscopic studies of peptides. Barriers to fragmentation as well as the associated overall energy differences are computed for the observed Calpha-C backbone bond cleavage as well as for side-chain loss for a variety of side chains (valine, arginine, glutamic acid, and tyrosine). It is found that Calpha-C bond cleavage is favored over side-chain loss, although loss of a tyrosine side chain may compete with Calpha-C cleavage because the tyrosine radical formed can delocalize its unpaired electron over its aromatic ring. In addition, it is found that fragmentation of the nitrogen-centered radicals formed in EDD results in cleavage to produce so-called a*/x fragments rather than a/x* fragments both because producing the former involves a significantly smaller barrier and is nearly thermoneutral, while cleavage to yield a/x* is significantly endothermic.

Journal Article↗
PubMed2005

Electron attachment step in electron capture dissociation (ECD) and electron transfer dissociation (ETD).

We have made use of classical dynamics trajectory simultions and ab initio electronic structure calculations to estimate the cross sections with which electrons are attached (in electron capture dissociation (ECD)) or transferred (in electron transfer dissociation (ETD)) to a model system that contained both an S-S bond that is cleaved and a -NH(3)(+) positively charged site. We used a Landau-Zener-Stueckelberg curve-crossing approximation to estimate the ETD rates for electron transfer from a CH(3)(-) anion to the -NH(3)(+) Rydberg orbital or the S-S sigma* orbital. We draw conclusions about ECD from our ETD results and from known experimental electron-attachment cross sections for cations and sigma-bonds. We predict the cross section for ETD at the positive site of our model compound to be an order of magnitude larger than that for transfer to the Coulomb-stabilized S-S bond site. We also predict that, in ECD, the cross section for electron capture at the positive site will be up to 3 orders of magnitude larger than that for capture at the S-S bond site. These results seem to suggest that attachment to such positive sites should dominate in producing S-S bond cleavage in our compound. However, we also note that cleavage induced by capture at the positive site will be diminished by an amount that is related to the distance from the positive site to the S-S bond. This dimunition can render cleavage through Coulomb-assisted S-S sigma* attachment competitive for our model compound. Implications for ECD and ETD of peptides and proteins in which SS or N-C(alpha) bonds are cleaved are also discussed, and we explain that such events are most likely susceptible to Coulomb-assisted attachment, because the S-S sigma* and C=O pi* orbitals are the lowest-lying antibonding orbitals in most peptides and proteins.

Algorithms↗
PubMed2005

Inverse potassium hydride: a theoretical study.

Results of an experimental study on the unusual "inverse" charge state (H(+)Na(-)) in salts where the H(+) ion is sequestered, combined with our earlier theoretical calculations on an unsequestered model compound (Me(3)N-H(+)...Na(-)), prompted us to further investigate such systems. In particular, we examined Et(3)N-H(+)...K(-) because considerations of the proton affinity of the amine and of the metal-hydride bond strength suggested that this ion-pair complex might be more stable to proton abstraction than was Me(3)N-H(+)...Na(-). In the present work, the ground-state potential energy surface of the Et(3)N-H(+)...K(-) ion pair was examined using second-order Møller-Plesset perturbation theory and 6-311++G basis sets. We found Et(3)N-H(+)...K(-) to be metastable to dissociation with a barrier of 8 kcal mol(-1) (computed at the CCSD(T) level of theory). This barrier indeed is substantially larger than that found earlier for (Me(3)N-H(+)...Na(-)) and suggests that unsequestered inverse-charged H(+)M(-) ion-pair salts may offer a reasonable route to creating high-energy materials if a means for synthesizing them in the laboratory can be designed.

Journal Article↗
PubMed2005

A theoretical model for indirect dissociative electron attachment.

In this paper, we describe a computational model that allows us to avoid having to perform a very large number of tedious calculations on electronically metastable anions when studying indirect DEA processes. By indirect, we mean that the electron attaches to an orbital in one region of the molecule but a bond is subsequently broken in another region. For such events, one must describe the coupling between two diabatic anion states, corresponding to the occupation of orbitals in the two regions of the molecule, to achieve a correct description. We introduce a simple 2 x 2 matrix model as well as physically reasonable and computationally efficient approximations to the diabatic states in regions where they are metastable. We show this model to be highly effective when applied to several indirect DEA processes that we studied earlier with brute-force methods. The main advantage of using this model is that one can avoid having to carry out a large number of calculations on metastable anion states; only one or two such calculations are required.

Journal Article↗
PubMed2005

Coulomb-assisted dissociative electron attachment: application to a model peptide.

The fragmentation of positively charged gas-phase samples of peptides is used to infer the primary structure of such molecules. In electron capture dissociation (ECD) experiments, very low-energy electrons attach to the sample and rupture bonds to effect the fragmentation. It turns out that ECD fragmentation tends to produce cleavage of very specific types of bonds. In earlier works by this group, it has been suggested that the presence of positive charges produces stabilizing Coulomb potentials that allow low-energy electrons to exothermically attach to sigma orbitals of certain bonds and thus to cleave those bonds. In the present effort, the stabilizing effects of Coulomb potentials due to proximal positive charges are examined for a small model peptide molecule that contains a wide range of bond types. Direct attachment of an electron to the sigma orbitals of eight different bonds as well as indirect sigma bond cleavage, in which an electron first binds to a carbonyl C=O pi orbital, are examined using ab initio methods. It is found that direct attachment to and subsequent cleavage of any of the eight sigma bonds is not likely except for highly positively charged samples. It is also found that attachment to a C=O pi orbital followed by cleavage of the nitrogen-to-alpha-carbon bond is the most likely outcome. Interestingly, this bond cleavage is the one that is seen most commonly in ECD experiments. So, the results presented here seem to offer good insight into one aspect of the ECD process, and they provide a means by which one can estimate (on the basis of a simple Coulomb energy formula) which bonds may be susceptible to cleavage by low-energy electron attachment.

Alanine↗
PubMed2005

Charge loss in gas-phase multiply negatively charged oligonucleotides.

In an attempt to shed light on the mechanism by which gaseous samples of negatively charged oligonucleotides undergo extremely slow (i.e., over 1-1000 s) charge loss, we have carried out molecular dynamics simulations on an oligonucleotide anion, T(5)(3-), containing five thymine, deoxyribose, and phosphate units in which the first, third, and fifth phosphates are negatively charged. The study is aimed at determining the rate at which an electron is detached from such a trianion by way of an internal Coulomb repulsion induced event. In this process, the intrinsic 5.0-5.1 eV electron binding strength of each phosphate site is reduced by the repulsive Coulomb potentials of the other two negative sites. As geometrical fluctuations cause the distances among the three negative phosphate sites to change, this causes the Coulomb repulsion energies at these sites to fluctuate. Once the Coulomb potential at any phosphate site exceeds ca. 5 eV, the electron on that site is able to undergo autodetachment. Although such an electron must tunnel through a barrier to escape, it is shown that the tunneling rate is not the rate-limiting step in electron loss; instead, it is the rate at which geometrical fluctuations cause the Coulomb potentials to exceed 5 eV that determines the rate of electron loss. Because these rates are extremely slow, special techniques had to be introduced to allow results of dynamics simulations on more flexible models of T(5)(3-) to be extrapolated to predict the behavior of the actual T(5)(3-).

Computer Simulation↗
PubMed2004

Damage to model DNA fragments from very low-energy (<1 eV) electrons.

Although electrons having enough energy to ionize or electronically excite DNA have long been known to cause strand breaks (i.e., bond cleavages), only recently has it been suggested that even lower-energy electrons (most recently 1 eV and below) can also damage DNA. The findings of the present work suggest that, while DNA bases can attach electrons having kinetic energies in the 1 eV range and subsequently undergo phosphate-sugar O-C sigma bond cleavage, it is highly unlikely (in contrast to recent suggestions) that electrons having kinetic energies near 0 eV can attach to the phosphate unit's P=O bonds. Electron kinetic energies in the 2-3 eV range are required to attach directly to DNA's phosphate group's P=O pi orbital and induce phosphate-sugar O-C sigma bond cleavages if the phosphate groups are rendered neutral (e.g., by nearby counterions). Moreover, significant activation barriers to C-O bond breakage render the rates of both such damage mechanisms (i.e., P=O-attached and base-attached) slow as compared to electron autodetachment and to other damage processes.

DNA Damage↗
PubMed2003

Theoretical analysis of the electronic structure and bonding stability of the TCNE dimer dianion (TCNE) 2 2-.

The (TCNE)(2)(2)(-) dimer dianion formed by connecting two TCNE(-) anions via a four-center, two-electron pi-orbital bond is studied using ab initio theoretical methods and a model designed to simulate the stabilization due to surrounding counterions. (TCNE)(2)(2)(-) is examined as an isolated species and in a solvation environment representative of tetrahydrofuran (THF) solvent. The intrinsic strength of this novel bond and the influences of internal Coulomb repulsions, of solvent stabilization and screening, and of counterion stabilization are all considered. The geometry, electronic and thermodynamic stabilities, electronic absorption spectra, and electron detachment energies of this novel dianion are examined to help understand recent experimental findings. Our findings lead us to conclude that the (TCNE)(2)(2)(-) dianion's observation in solid materials is likely a result of its stabilization by surrounding countercations. Moreover, our results suggest the dianion is geometrically metastable in THF solution, with a barrier to dissociation into two TCNE(-) anions that can be quickly surmounted at room temperature but not at 77 K. This finding is consistent with what is observed in laboratory studies of low- and room-temperature solutions of salts containing this dianion. Finally, we assign two peaks observed (at 77 K in methyl-THF glass) in the UV-vis region to (1) electronic transitions involving the four-center orbitals and (2) detachment of an electron from the four-center pi-bonding orbital to generate (TCNE)(2)(-) + e(-).

Journal Article↗
PubMed2003

Chemical reduction of 2,4,6-tricyano-1,3,5-triazine and 1,3,5-tricyanobenzene. Formation of novel 4,4',6,6'-Tetracyano-2,2'-bitriazine and its radical anion.

Chemical reduction of 2,4,6-tricyano-1,3,5-triazine, TCT, results in the formation of an unstable radical anion that undergoes immediate dimerization at a ring carbon to form [C(12)N(12)](2-), [TCT](2)(2-), characterized by a long 1.570 (4) A central C[bond]C. [TCT](2)(2-) can decompose into the radical anion of 4,4',6,6'-tetracyano-2,2'-bitriazine, [TCBT]*-, the one-electron reduced form of planar (D(2h)) TCBT, which is also structurally characterized as the [TMPD][TCBT] charge-transfer complex (TMPD = N,N,N',N'-tetramethyl-p-phenylenediamine) with a 1.492 (2) A central sp(2)[bond]sp(2) C[bond]C. Although crystals could not be obtained for the radical anion [TCBT]*-, the electrochemistry (E degrees = +0.03 V), EPR (g = 2.003, (2)A((14)N) = 3.347 G, and (4)A((14)N) = 0.765 G and a line width of 0.24 G), and theoretical calculations support the formation of [TCBT]*-. In addition, thermolysis of [TCT](2)(2-) yields [TCBT]*-. Chemical reduction of 2,4,6-tricyanobenzene, TCB, forms an unstable radical anion that immediately undergoes dimerization at a ring carbon to form [C(12)H(6)N(6)](2-), [TCB](2)(2-), which has a long 1.560 (5) A central C[bond]C. Reaction of TCT with tetrathiafulvalene (TTF) forms structurally characterized [TTF][TCT], and in the presence of water, TCT hydrolyzes to 2,4-dicyano-6-hydroxy-s-triazine, DCTOH. In contrast, the reaction of TCT with TMPD forms [TMPD][TCT], which in the presence of water forms structurally characterized [HTMPD](+)[DCTO](-).

Journal Article↗
PubMed2003

Inverse sodium hydride: a theoretical study.

A recent experimental investigation in which a salt containing the unusual charge distribution H(+) and Na(-) was synthesized and characterized prompted us to undertake an ab initio theoretical investigation. In the salt synthesized, the H(+) is bound to the nitrogen center of an amine and the Na(-) alkalide is "blocked" from approaching the protonated amine site by steric constraints of a cage structure. Although one expects that the Na(-) would deprotonate an unprotected R(3)N-H(+) cation, we decided to further explore this issue. Using extended atomic orbital basis sets and Møller-Plesset and coupled-cluster treatments of electron correlation, we examined the relative stabilities of the prototype (Me)(3)N + NaH, (Me)(3)N + Na(+) + H(-), (Me)(3)N-H(+) + Na(-), and (Me)(3)N-Na(+) + H(-) as well as the ion pair complexes (Me)(3)N-H(+).Na(-) and (Me)(3)N-Na(+).H(-). The primary focus of this effort was to determine whether the high-energy (Me)(3)N-H(+).Na(-) ion pair, which is the analogue of what the earlier workers termed "inverse sodium hydride", might be stable with respect to proton abstraction under any reasonable solvation conditions (which we treated within the polarized continuum model). Indeed, we find that such ion pairs are metastable (i.e., locally geometrically stable with a barrier to dissociation) for solvents having dielectric constants below approximately 2 but spontaneously decompose into their constituent ions for solvents with higher dielectric constants. We suggest that amines with large proton affinities and/or metals with weaker MH bond strengths should be explored experimentally.

Journal Article↗