Dative Bonding in Quasimetallatranes Containing Group 15 Donors (Y = N, P, and As) and Group 14 Acceptors (M = Si, Ge, Sn, and Pb).

Metallatranes and their analogous fused ring [3.3.0] bicyclic compounds, quasimetallatranes, have emerged as fascinating molecular systems with intriguing structural, bonding, and conformational properties. We present a comprehensive investigation aimed at unraveling the nature of dative bonding and exploring the conformational flexibility of these compounds. We extensively characterize the dative bond between the metal center and the electron pair donor, using a range of modeling techniques. Our analyses involve structural optimizations, molecular orbital examinations, and covalency ratio calculations, which provide a thorough understanding of the bonding interactions responsible for the stability of these systems. The results confirmed the presence of dative bonds, supported by the close proximity between the metal and the electron-donating group, and the observation of overlapping electron density. Our studies reveal a correlation between the size of the electron-donor and the coordinating metal atom, and the strength of the dative interaction, as indicated by the bond length and the Wiberg bond indices. This bond strength, in turn, influences the conformational preferences adopted by these compounds. This investigation sheds light on the fundamental aspects of the fused ring [3.3.0] bicyclic quasimetallatrane compounds and offers valuable insights into their unique properties.

Multireference Averaged Quadratic Coupled Cluster (MR-AQCC) Study of the Geometries and Energies for ortho-, meta- and para-Benzyne.

The diradical benzyne isomers are excellent prototypes for evaluating the ability of an electronic structure method to describe static and dynamic correlation. The benzyne isomers are also interesting molecules with which to study the fundamentals of through-space and through-bond diradical coupling that is important in so many electronic device applications. In the current study, we utilize the multireference methods MC-SCF, MR-CISD, MR-CISD+Q, and MR-AQCC with an (8,8) complete active space that includes the σ, σ*, π and π* orbitals, to characterize the electronic structure of ortho-, meta- and para-benzyne. We also determine the adiabatic and vertical singlet-triplet splittings for these isomers. MR-AQCC and MR-CISD+Q produced energy gaps in good agreement with previously obtained experimental values. Geometries, orbital energies and unpaired electron densities show significant through-space coupling in the o- and m-benzynes, while p-benzyne shows through-bond coupling, explaining the dramatically different singlet-triplet gaps between the three isomers.

Variations on the Bergman Cyclization Theme: Electrocyclizations of Ionic Penta-, Hepta-, and Octadiynes.

The Bergman cyclization of (Z)-hexa-3-ene-1,5-diyne to form the aromatic diradical p-benzyne has garnered attention as a potential antitumor agent due to its relatively low cyclization barrier and the stability of the resulting diradical. Here, we present a theoretical investigation of several ionic extensions of the fundamental Bergman cyclization: electrocyclizations of the penta-1,4-diyne anion, hepta-1,6-diyne cation, and octa-1,7-diyne dication, leveraging the spin-flip formulation of the equation-of-motion coupled cluster theory with single and double substitutions (EOM-SF-CCSD). Though the penta-1,4-diyne anion exhibits a large cyclization barrier of +66 kcal mol-1, cyclization of both the hepta-1,6-diyne cation and octa-1,7-diyne dication along a previously unreported triplet pathway requires relatively low energy. We also identified the presence of significant aromaticity in the triplet diradical products of these two cationic cyclizations.

Experimental and Theoretical Study of Oxolan-3-one Thermal Decomposition.

The thermal decomposition of oxolan-3-one, a common component of the bio-oil formed during biomass pyrolysis, has been studied using ab initio calculations and experiments employing pulsed gas-phase pyrolysis with matrix-isolation FTIR product detection. Four pathways for unimolecular decomposition were predicted using computational methods. The dominant reaction channel led to carbon monoxide, formaldehyde, and ethylene, all of which were observed experimentally. The other channels led to an assortment of products including ketene, water, propyne, and acetylene, which were all confirmed in the matrix-isolation FTIR spectra. There is also evidence for the production of substituted ketenes in pyrolysis, most likely hydroxyketene and methylketene.

Understanding the Structure and Apo Dynamics of the Functionally Active JIP1 Fragment.

Recent experiments indicate that the C-Jun amino-terminal kinase-interacting protein 1 (JIP1) binds to and activates the c-Jun N-terminal kinase (JNK) protein. JNK is an integral part of cell apoptosis, and misregulation of this process is a causative factor in diseases such as Alzheimer's disease (AD), obesity, and cancer. It has also been shown that JIP1 may increase the phosphorylation of tau by facilitating the interaction between the tau protein and JNK, which could also be a causative factor in AD. Very little is known about the structure and dynamics of JIP1; however, the amino acid composition of the first 350 residues suggests that it contains an intrinsically disordered region. Molecular dynamics (MD) simulations using AMBER 14 were used to study the structure and dynamics of a functionally active JIP1 10mer fragment to better understand the solution behavior of the fragment. Two microseconds of unbiased MD was performed on the JIP1 10mer fragment in 10 different seeds for a total of 20 µs of simulation time, and from this, seven structurally stable conformations of the 10mer fragment were identified via classical clustering. The 10mer ensemble was also used to build a Markov state model (MSM) that identified four metastable states that encompassed six of the seven conformational families identified by classical dimensional reduction. Based on this MSM, conformational interconversions between the four states occur via two dominant pathways with probability fluxes of 55 and 44% for each individual pathway. Transitions between the initial and final states occur with mean first passage times of 31 (forward) and 16 (reverse) µs.

Evaluating Halogen-Bond Strength as a Function of Molecular Structure Using Nuclear Magnetic Resonance Spectroscopy and Computational Analysis.

Halogen bonding (XB) is a highly directional, non-covalent intermolecular interaction between a molecule (XB donor) presenting a halogen with an electron-deficient region or sigma hole (σ-hole) and an electron-rich or Lewis-base molecule (XB acceptor). A systematic, experimental, and theoretical study of solution-phase XB strength as a function of the molecular structure for both XB donor and acceptor molecules is presented. The impact of specific structural features is assessed using 19F and 1H nuclear magnetic resonance (NMR) titrations to determine association constants, density functional theory calculations for interaction energies and bond lengths, as well as 19F-1H HOESY NMR measurements of intermolecular cross-relaxation between the interacting XB donor-acceptor adducts. For XB donor molecules (perfluoro-halogenated benzenes), results indicate the critical importance of iodine coupled with electron-withdrawing entities. Prominent structural components of XB acceptor molecules include a central atom working in conjunction with a Lewis-base atom to present high electron density directed at the σ-hole (e.g., tributylphosphine oxide). Additionally, larger surrounding aliphatic R groups (e.g., butyl and octyl) were found to significantly stabilize strong XB, particularly in solvents that promote the interaction. With a more thorough understanding of structure-optimized XB, one can envision harnessing XB interactions more strategically for specific design of optimal materials and chemical applications.

Isofunctional Clustering and Conformational Analysis of the Arsenate Reductase Superfamily Reveals Nine Distinct Clusters.

Arsenate reductase (ArsC) is a superfamily of enzymes that reduce arsenate. Due to active site similarities, some ArsC can function as low-molecular weight protein tyrosine phosphatases (LMW-PTPs). Broad superfamily classifications align with redox partners (Trx- or Grx-linked). To understand this superfamily's mechanistic diversity, the ArsC superfamily is classified on the basis of active site features utilizing the tools TuLIP (two-level iterative clustering process) and autoMISST (automated multilevel iterative sequence searching technique). This approach identified nine functionally relevant (perhaps isofunctional) protein groups. Five groups exhibit distinct ArsC mechanisms. Three are Grx-linked: group 4AA (classical ArsC), group 3AAA (YffB-like), and group 5BAA. Two are Trx-linked: groups 6AAAAA and 7AAAAAAAA. One is an Spx-like transcriptional regulatory group, group 5AAA. Three are potential LMW-PTP groups: groups 7BAAAA, and 7AAAABAA, which have not been previously identified, and the well-studied LMW-PTP family group 8AAA. Molecular dynamics simulations were utilized to explore functional site details. In several families, we confirm and add detail to literature-based mechanistic information. Mechanistic roles are hypothesized for conserved active site residues in several families. In three families, simulations of the unliganded structure sample specific conformational ensembles, which are proposed to represent either a more ligand-binding-competent conformation or a pathway toward a more binding-competent state; these active sites may be designed to traverse high-energy barriers to the lower-energy conformations necessary to more readily bind ligands. This more detailed biochemical understanding of ArsC and ArsC-like PTP mechanisms opens possibilities for further understanding of arsenate bioremediation and the LMW-PTP mechanism.

The generality of the GUGA MRCI approach in COLUMBUS for treating complex quantum chemistry.

The core part of the program system COLUMBUS allows highly efficient calculations using variational multireference (MR) methods in the framework of configuration interaction with single and double excitations (MR-CISD) and averaged quadratic coupled-cluster calculations (MR-AQCC), based on uncontracted sets of configurations and the graphical unitary group approach (GUGA). The availability of analytic MR-CISD and MR-AQCC energy gradients and analytic nonadiabatic couplings for MR-CISD enables exciting applications including, e.g., investigations of π-conjugated biradicaloid compounds, calculations of multitudes of excited states, development of diabatization procedures, and furnishing the electronic structure information for on-the-fly surface nonadiabatic dynamics. With fully variational uncontracted spin-orbit MRCI, COLUMBUS provides a unique possibility of performing high-level calculations on compounds containing heavy atoms up to lanthanides and actinides. Crucial for carrying out all of these calculations effectively is the availability of an efficient parallel code for the CI step. Configuration spaces of several billion in size now can be treated quite routinely on standard parallel computer clusters. Emerging developments in COLUMBUS, including the all configuration mean energy multiconfiguration self-consistent field method and the graphically contracted function method, promise to allow practically unlimited configuration space dimensions. Spin density based on the GUGA approach, analytic spin-orbit energy gradients, possibilities for local electron correlation MR calculations, development of general interfaces for nonadiabatic dynamics, and MRCI linear vibronic coupling models conclude this overview.

A Molecular Dynamics Investigation of the Thermostability of Cold-Sensitive I707L KlenTaq1 DNA Polymerase and Its Wild-Type Counterpart.

DNA polymerase I from Thermus aquaticus ( Taq DNA polymerase) is useful for polymerase chain reactions because of its exceptional thermostability; however, its activity at low temperatures can cause amplification of unintended products. Mutation of isoleucine 707 to leucine (I707L) slows Taq DNA polymerase at low temperatures, which decreases unwanted amplification due to mispriming. In this work, unrestrained molecular dynamics (MD) simulations were performed on I707L and wild-type (WT) Taq DNA polymerase at 341 and 298 K to determine how the mutation affects the dynamic nature of the protein. The results suggest that I707L Taq DNA polymerase remains relatively immobile at room temperature and becomes more flexible at the higher temperature, while the WT Taq DNA polymerase demonstrates less substantial differences in dynamics at high and low temperatures. These results are in agreement with previous experimental results on the I707L mutant Taq DNA polymerase that show dynamic differences at high and low temperatures. The decreased mobility of the mutant at low temperature suggests that the mutant remains longer in the blocked conformation, and this may lead to reduced activity relative to the WT at 298 K. Principal component analysis revealed that the mutation results in decoupled movements of the Q helix and fingers domain. This decoupled nature of the mutant gives way to an increasingly flexible N-terminal end of the Q helix at 341 K, a characteristic not seen for WT Taq DNA polymerase.

A Multireference Ab Initio Study of the Diradical Isomers of Pyrazine.

Three diradical pyrazine isomers were characterized using highly correlated, multireference methods. The lowest lying singlet and triplet state geometries of 2,3-didehydropyrazine ( ortho), 2,5-didehydropyrazine ( para), and 2,6-didehydropyrazine ( meta) were determined. Two active reference spaces were utilized. The complete active space (CAS) (8,8) includes the σ and σ* orbitals on the dehydrocarbon atoms as well as the valence π and π* orbitals. The CAS (12,10) reference space includes two additional orbitals corresponding to the in-phase and out-of-phase nitrogen lone pair orbitals. Adiabatic and vertical gaps between the lowest lying singlet and triplet states, optimized geometries, canonicalized orbital energies, unpaired electron densities, and spin polarization effects were compared. We find that the singlet states of each diradical isomer contain two significantly weighted configurations, and the larger active space is necessary for the proper physical characterization of both the singlet and triplet states. The singlet-triplet splitting is very small for the 2,3-didehydropyrazine ( ortho) and 2,6-didehydropyrazine ( meta) isomers (+1.8 and -1.4 kcal/mol, respectively) and significant for the 2,5-didehydropyrazine ( para) isomer (+28.2 kcal/mol). Singlet geometries show through-space interactions between the dehydocarbon atoms in the 2,3-didehydropyrazine ( ortho) and 2,6-didehydropyrazine ( meta) isomers. An analysis of the effectively unpaired electrons suggests that the 2,5-didehydropyrazine ( para) isomer also displays through-bond coupling between the diradical electrons.

Analysis of MEMO1 Binding Specificity for ErbB2 Using Fluorescence Polarization and Molecular Dynamics Simulations.

ErbB2 signaling pathways are linked to breast cancer formation, growth, and aggression; therefore, understanding the behavior of proteins associated with these pathways as well as regulatory factors that influence ErbB2 function is essential. MEMO1 is a redox active protein that is shown to associate with phosphorylated ErbB2 and mediate cell motility. We have developed a fluorescence polarization assay to probe the interaction between MEMO1 and an ErbB2-derived peptide containing a phosphorylated tyrosine residue. This interaction is shown to be pH-dependent and stronger with longer peptides as would be expected for protein-protein interactions. We have quantitatively mapped the binding interface of MEMO1 to the peptide using the fluorescence polarization assay and molecular dynamics simulations. We have confirmed that phosphorylation of the peptide is essential for binding and through mutagenesis have identified residues that contribute to favorable interactions. Our results highlight the importance of the protein-protein interactions of MEMO1 that complement the oxidase activity. In the future, these studies will provide a method for screening for selective modulators of MEMO1, which will allow for additional biological investigations.

A Computational Study of the Reactivity of 3,5-(Oxo/Thioxo) Derivatives of 2,7-Dimethyl-1,2,4-Triazepines. Keto-Enol Tautomerization and Potential for Hydrogen Storage.

The G4 level of theory was used to evaluate the acidity of a series of triazepines, that is, 3-thioxo-5-oxo-, 5-thioxo-3-oxo-, 3,5-dioxo-, and 3,5-dithioxo- derivatives of 2,7-dimethyl-[1,2,4]-triazepine. The ability of their available nitrogen lone pair to form a dative bond with BH3 was also studied to highlight the resulting changes in acidity and to understand the behavior of the complexes formed. The effect of the substitution of sulfur by oxygen on the stability of the complex and the activation barrier of dehydrogenation was also evaluated. The formation of these triazepine:BH3 complexes, accompanied by the loss of H2 molecular hydrogen, is a strongly exothermic process. With one triazepine the pathway for H2 elimination from [triazepine]-BH3 is characterized by a small energy barrier ranging from 11 to 23 kJ/mol. The second H2 elimination is relatively more energetic than the first one (∼27 kJ/mol). Because of the steric hindrance associated with the addition of two molecules of triazepine (triazepine)2-BH2, the third dehydrogenation step is relatively less favorable than the two preceding steps, particularly in the case of the 3,5-dithio- derivative. The potential energy surface associated with the dehydrogenation reaction of all triazepine derivatives was explored. The thermodynamic favorability reported in this study could allow triazepine-borane to be used as a material for H2 storage applications.

An Extended Multireference Study of the Singlet and Triplet States of the 9,10-didehydroanthracene Diradical.

The 9,10-didehydroanthracene is an aromatic diradical produced by the Bergman cyclization of a benzannulated 10-membered enediyne. It is a 1,4 diradical, similar to p-benzyne. Here we study the spin state occupancy of the ground state of 9,10-didehydroanthracene by employing multireference methods (MR-CISD and MR-AQCC) with different basis sets (cc-pVDZ and cc-pVTZ) and active space sizes (CAS (2,2) through CAS (8,8)). At the CAS (8,8) MR-AQCC/cc-pVDZ level of theory, we find a two-configurational singlet ground state with an adiabatic Δ EST of 6.13 kcal/mol. Unpaired electron density populations and dominant electronic configuration interactions were used to analyze the features of the 9,10-didehydroanthracene diradical.

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.

A molecular dynamics study of the binary complexes of APP, JIP1, and the cargo binding domain of KLC.

Mutations in the amyloid precursor protein (APP) are responsible for the formation of amyloid-ß peptides. These peptides play a role in Alzheimer's and other dementia-related diseases. The cargo binding domain of the kinesin-1 light chain motor protein (KLC1) may be responsible for transporting APP either directly or via interaction with C-jun N-terminal kinase-interacting protein 1 (JIP1). However, to date there has been no direct experimental or computational assessment of such binding at the atomistic level. We used molecular dynamics and free energy estimations to gauge the affinity for the binary complexes of KLC1, APP, and JIP1. We find that all binary complexes (KLC1:APP, KLC1:JIP1, and APP:JIP1) contain conformations with favorable binding free energies. For KLC1:APP the inclusion of approximate entropies reduces the favorability. This is likely due to the flexibility of the 42-residue APP protein. In all cases we analyze atomistic/residue driving forces for favorable interactions. Proteins 2017; 85:221-234. © 2016 Wiley Periodicals, Inc.

Modeling Oil Shale Pyrolysis: High-Temperature Unimolecular Decomposition Pathways for Thiophene.

The thermal decomposition mechanism of thiophene has been investigated both experimentally and theoretically. Thermal decomposition experiments were done using a 1 mm × 3 cm pulsed silicon carbide microtubular reactor, C4H4S + Δ â†’ Products. Unlike previous studies these experiments were able to identify the initial thiophene decomposition products. Thiophene was entrained in either Ar, Ne, or He carrier gas, passed through a heated (300-1700 K) SiC microtubular reactor (roughly ≤100 µs residence time), and exited into a vacuum chamber. The resultant molecular beam was probed by photoionization mass spectroscopy and IR spectroscopy. The pyrolysis mechanisms of thiophene were also investigated with the CBS-QB3 method using UB3LYP/6-311++G(2d,p) optimized geometries. In particular, these electronic structure methods were used to explore pathways for the formation of elemental sulfur as well as for the formation of H2S and 1,3-butadiyne. Thiophene was found to undergo unimolecular decomposition by five pathways: C4H4S → (1) S═C═CH2 + HCCH, (2) CS + HCCCH3, (3) HCS + HCCCH2, (4) H2S + HCC-CCH, and (5) S + HCC-CH═CH2. The experimental and theoretical findings are in excellent agreement.

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.

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.

Jahn-Teller distortion in polyoligomeric silsesquioxane (POSS) cations.

We investigated the symmetry breaking mechanism in cubic octa-tert-butyl silsesquioxane and octachloro silsesquioxane monocations (Si8O12(C(CH3)3)8(+) and Si8O12Cl8(+)) using density functional theory (DFT) and group theory. Under Oh symmetry, these ions possess (2)T2g and (2)Eg electronic states and undergo different symmetry breaking mechanisms. The ground states of Si8O12(C(CH3)3)8(+) and Si8O12Cl8(+) belong to the C3v and D4h point groups and are characterized by Jahn-Teller stabilization energies of 3959 and 1328 cm(-1), respectively, at the B3LYP/def2-SVP level of theory. The symmetry distortion mechanism in Si8O12Cl8(+) is Jahn-Teller type, whereas in Si8O12(C(CH3)3)8(+) the distortion is a combination of both Jahn-Teller and pseudo-Jahn-Teller effects. The distortion force acting in Si8O12(C(CH3)3)8(+) is mainly localized on one Si-(tert-butyl) group, while in Si8O12Cl8(+) it is distributed over the oxygen atoms. The main distortion forces acting on the Si8O12 core arise from the coupling between the electronic state and the vibrational modes, identified as 9t2g + 1eg + 3a2u for the Si8O12(C(CH3)3)8(+) and 1eg + 2eg for Si8O12Cl8(+).