Carol A. Parish

Halogen Bonding in DNA Base Pairs

Halogen bonding (R-X···Y) is a qualitative analogue of hydrogen bonding that may prove useful in the rational design of artificial proteins and nucleotides. We explore halogen-bonded DNA base pairs containing modified guanine, cytosine, adenine and thymine nucleosides. The structures and stabilities of the halogenated systems are compared to the normal hydrogen bonded base pairs. In most cases, energetically stable, coplanar structures are identified. In the most favorable cases, halogenated base pair stabilities are within 2 kcal mol(-1) of the hydrogen bonded analogues. Among the halogens X = Cl, Br, and I, bromine is best suited for inclusion in these biological systems because it possesses the best combination of polarizability and steric suitability. We find that the most stable structures result from a single substitution of a hydrogen bond for a halogen bond in dA:dT and dG:dC base pairs, which allows 1 or 2 hydrogen bonds, respectively, to complement the halogen bond.

Pairwise and many-body contributions to interaction potentials in Hen clusters

High level ab initio calculations have been carried out to assess the pairwise additivity of potentials in the attractive or well regions of the potential surfaces of clusters of helium atoms. A large basis set was employed and calculations were done at the Brueckner orbital coupled cluster level. Differences between calculated potentials for several interacting atoms and the corresponding summed pair potentials reveal the three‐body and certain higher order contributions to the interaction strengths. Attraction between rare gas atoms develops from dispersion, and so helium clusters provide the most workable systems for analyzing nonadditivity of dispersion. The results indicate that the many‐body or nonpairwise contributions tend to be less than a few percent of the attractive interaction across regions around the minima of the potential energy surfaces of small clusters. Dipole–dipole–dipole dispersion and dipole–dipole–quadrupole dispersion are noticeable parts of the small three‐body terms.

An extended multireference study of the electronic states of para-benzyne.

A state-averaged, multireference complete active space (CAS) approach was used for the determination of the vertical excitation energies of valence and Rydberg states of para-benzyne. Orbitals were generated with a 10- and 32-state averaged multiconfigurational self-consistent field approach. Electron correlation was included using multireference configuration interaction with singles and doubles, including the Pople correction for size extensivity, multireference averaged quadratic coupled cluster (MR-AQCC), and MR-AQCC based on linear response theory. There is a very high density of electronic states in this diradical system-there are more than 17 states within 7 eV of the ground state including two 3s Rydberg states. All excitations, except 2 (1)A(g), are from the pi system to the sigmasigma(*) system. Of the 32 states characterized, 15 were multiconfigurational, including the ground (1)A(g) state, providing further evidence for the necessity of a multireference approach for p-benzyne. The vertical singlet-triplet splitting was also characterized using a two-state averaged approach. A CAS(2,2) calculation was shown to be inadequate due to interaction with the pi orbitals.

Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I

During DNA replication, DNA polymerases follow an induced fit mechanism in order to rapidly distinguish between correct and incorrect dNTP substrates. The dynamics of this process are crucial to the overall effectiveness of catalysis. Although X-ray crystal structures of DNA polymerase I with substrate dNTPs have revealed key structural states along the catalytic pathway, solution fluorescence studies indicate that those key states are populated in the absence of substrate. Herein, we report the first atomistic simulations showing the conformational changes between the closed, open, and ajar conformations of DNA polymerase I in the binary (enzyme∶DNA) state to better understand its dynamics. We have applied long time-scale, unbiased molecular dynamics to investigate the opening process of the fingers domain in the absence of substrate for B. stearothermophilis DNA polymerase in silico. These simulations are biologically and/or physiologically relevant as they shed light on the transitions between states in this important enzyme. All closed and ajar simulations successfully transitioned into the fully open conformation, which is known to be the dominant binary enzyme-DNA conformation from solution and crystallographic studies. Furthermore, we have detailed the key stages in the opening process starting from the open and ajar crystal structures, including the observation of a previously unknown key intermediate structure. Four backbone dihedrals were identified as important during the opening process, and their movements provide insight into the recognition of dNTP substrate molecules by the polymerase binary state. In addition to revealing the opening mechanism, this study also demonstrates our ability to study biological events of DNA polymerase using current computational methods without biasing the dynamics.

A comparison of the Low Mode and Monte Carlo conformational search methods

The Low Mode (LM) and Monte Carlo (MC) conformational search methods were compared on three diverse molecular systems; (4R, 5S, 6S, 7R)-hexahydro-5,6-dihydroxy-1,3,4,7-tetrakis(phenylmethyl)-2H-1,3-diazapin-2-one (1), 2-methoxy-2-phenyl-2-triflouromethyl-N-alpha-methyl benzyl propanamide (2) and a trimeric 39-membered polyazamacrolide (3). We find that either method, or a combination of the methods, is equally efficient at searching the conformational space of the smaller molecular systems while a 50:50 hybrid of Low Mode and Monte Carlo is most efficient at searching the space of the larger molecular system.

Three‐body analytical potential for interacting helium atoms

Large basis set ab initio calculations have been carried out for a dense grid of points on the He3 potential energy surface. Three‐body contributions were extracted at every point, and a number of concise functional representations for the three‐body potential surface were then examined. Three‐body multipolar dispersion terms and other radial and angular terms were used in the representations, and an assessment of relative importance of the different terms is presented. Combined with a two‐body He–He potential, the results of this work should offer a high quality interaction potential for simulations of aggregated helium.

Mechanisms for the Reaction of Thiophene and Methylthiophene with Singlet and Triplet Molecular Oxygen

Mechanisms for the reaction of thiophene and 2-methylthiophene with molecular oxygen on both the triplet and singlet potential energy surfaces (PESs) have been investigated using ab initio methods. Geometries of various stationary points involved in the complex reaction routes are optimized at the MP2/6-311++G(d, p) level. The barriers and energies of reaction for all product channels were refined using single-point calculations at the G4MP2 level of theory. For thiophene, CCSD(T) single point energies were also determined for comparison with the G4MP2 energies. Thiophene and 2-methylthiophene were shown to react with O(2) via two types of mechanisms, namely, direct hydrogen abstraction and addition/elimination. The barriers for reaction with triplet oxygen are all significantly large (i.e., >30 kcal mol(-1)), indicating that the direct oxidation of thiophene by ground state oxygen might be important only in high temperature processes. Reaction of thiophene with singlet oxygen via a 2 + 4 cycloaddition leading to endoperoxides is the most favorable channel. Moreover, it was found that alkylation of the thiophene ring (i.e., methyl-substituted thiophene) is capable of lowering the barrier height for the addition pathway. The implication of the current theoretical results may shed new light on the initiation mechanisms for combustion of asphaltenes.

Pyrolysis mechanisms of thiophene and methylthiophene in asphaltenes.

The pyrolysis mechanisms of thiophene in asphaltenes have been investigated theoretically using density functional and ab initio quantum chemical techniques. All of the possible reaction pathways were explored using B3LYP, MP2, and CBS-QB3 models. A comparison of the calculated heats of reaction with the available experimental values indicates that the CBS-QB3 level of theory is quantitatively reliable for calculating the energetic reaction paths of the title reactions. The pyrolysis process is initiated via four different types of hydrogen migrations. According to the reaction barrier heights, the dominant 1,2-H shift mechanism involves two competitive product channels, namely, C(2)H(2) + CH(2)CS and CS + CH(3)CCH. The minor channels include the formation of CS + CH(2)CCH(2), H(2)S + C(4)H(2), HCS + CH(2)CCH, CS + CH(2)CHCH, H + C(4)H(3)S, and HS + C(4)H(3). The methyl substitution effect was investigated with the pyrolysis of 2-methylthiophene and 3-methylthiophene. The energetics of such systems were very similar to that for unsubstituted thiophene, suggesting that thiophene alkylation may not play a significant role in the pyrolysis of asphaltene compounds.

A conservative isoleucine to leucine mutation causes major rearrangements and cold sensitivity in KlenTaq1 DNA polymerase.

Assembly of polymerase chain reactions at room temperature can sometimes lead to low yields or unintentional products due to mispriming. Mutation of isoleucine 707 to leucine in DNA polymerase I from Thermus aquaticus substantially decreases its activity at room temperature without compromising its ability to amplify DNA. To understand why a conservative change to the enzyme over 20 Å from the active site can have a large impact on its activity at low temperature, we solved the X-ray crystal structure of the large (5′-to-3′ exonuclease-deleted) fragment of Taq DNA polymerase containing the cold-sensitive mutation in the ternary (E–DNA–ddNTP) and binary (E–DNA) complexes. The I707L KlenTaq1 ternary complex was identical to the wild-type in the closed conformation except for the mutation and a rotamer change in nearby phenylalanine 749, suggesting that the enzyme should remain active. However, soaking out of the nucleotide substrate at low temperature results in an altered binary complex made possible by the rotamer change at F749 near the tip of the polymerase O-helix. Surprisingly, two adenosines in the 5′-template overhang fill the vacated active site by stacking with the primer strand, thereby blocking the active site at low temperature. Replacement of the two overhanging adenosines with pyrimidines substantially increased activity at room temperature by keeping the template overhang out of the active site, confirming the importance of base stacking. These results explain the cold-sensitive phenotype of the I707L mutation in KlenTaq1 and serve as an example of a large conformational change affected by a conservative mutation.

An ab Initio Exploration of the Bergman Cyclization

The Bergman cyclization is an important reaction in which an enediyne cyclizes to produce a highly reactive diradical species, p-benzyne. Enediyne motifs are found in natural antitumor antibiotic compounds, such as calicheammicin and dynemicin. Understanding the energetics of cyclization is required to better control the initiation of the cyclization, which induces cell death. We computed the singlet and triplet potential energy surfaces for the Bergman cyclization of (Z)-hex-3-ene-1,5-diyne using the CCSD and EOM-SF-CCSD methods. The triplet enediyne and transition state were found to have C2 symmetry, which contrasts with the singlet reactant and transition state that possess C2v symmetry. We analyzed the frontier orbitals of both cyclization pathways to explain the large energetic barrier of the triplet cyclization. Reaction energies were calculated using CCSD(T)/cc-pVTZ single-point calculations on structures optimized with CCSD/cc-pVDZ. The singlet reaction was found to be slightly endothermic (ΔHrxn = 13.76 kcal/mol) and the triplet reaction was found to be highly exothermic (ΔHrxn = -33.29 kcal/mol). The adiabatic singlet-triplet gap of p-benzyne, computed with EOM-SF-CCSD/cc-pVTZ, was found to be 3.56 kcal/mol, indicating a singlet ground state.