Biomedical subjects

Piotr Skurski

Publications and source records attributed to Piotr Skurski.

12 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

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↗

PubMed2005

Negatively charged xanthine. I. Anions formed by canonical isomers.

The possibility of an excess electron binding to canonical isomers of xanthine in the gas phase was studied at the coupled-cluster level with single and double excitations using the 6-31++G** basis sets supplemented with the 4(sp)3d set of diffuse functions. It was found that xanthine should exist in the gas phase as one canonical tautomer while all the other tautomers are not likely to be detected experimentally because of their significant thermodynamic instability. On the other hand, all canonical tautomers (except one) were found to be capable of forming electronically stable anionic states of dipole-bound nature. However, the only thermodynamically stable anion (with vertical electron binding energy estimated to be 0.041 eV) based on xanthine tautomers is the one supported by the most stable neutral species.

Anions↗

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

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

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↗

PubMed1999

Toward an Understanding of the Chemiluminescence Accompanying the Reaction of 9-Carboxy-10-methylacridinium Phenyl Ester with Hydrogen Peroxide.

The reaction between 9-carboxy-10-methylacridinium phenyl ester (CMAPE) and hydrogen peroxide leading to the formation of electronically excited 10-methyl-9-acridinone has been examined at the semiempirical PM3 level of theory. The reaction mechanisms proposed in the literature were verified and the details of the rather complicated processes leading to the emission of light (chemiluminescence) explained by these theoretical studies. Particular reaction steps were characterized at the thermodynamic and kinetic levels. The influence of the solvent was studied by means of the PM3-COSMO method (aqueous medium). The bottleneck steps determining the kinetics of the overall process were identified. Structural modifications of CMAPE that could improve its analytical usefulness were indicated on the basis of theoretical considerations.

Journal Article↗