Theoretical Appraisal of Cyclopropenone: Aggregation and Complexes with Water.

Cyclopropenone (HCCOCH, "CPN") is an exotic quasi-aromatic cyclic carbene that abounds in the interstellar medium (ISM). Astronomical observations suggest that (i) stagnate CPN exhibits a tendency to polymerize and that (ii) interactions may occur between CPN and water that is also ubiquitous in the ISM. In this light, density functional theory investigations reveal cooperative hydrogen bonding, which leads to stable polymeric conformations of (CPN), tracked up to = 14.

Mechanistic Investigation of Site-specific DNA Methylating Agents Targeting Breast Cancer Cells.

We previously described the development of a DNA-alkylating compound that showed selective toxicity in breast cancer cells. This compound contained an estrogen receptor α (ERα)-binding ligand and a DNA-binding/methylating component that could selectively methylate the N3-position of adenines at adenine-thymine rich regions of DNA. Herein, we describe mechanistic investigations that demonstrate that this class of compounds facilitate the translocation of the ERα-compound complex to the nucleus and induce the expression of ERα target genes.

Impact of Local Electrostatics on the Redox Properties of Tryptophan Radicals in Azurin: Implications for Redox-Active Tryptophans in Proton-Coupled Electron Transfer.

Tyrosine and tryptophan play critical roles in facilitating proton-coupled electron transfer (PCET) processes essential to life. The local protein environment is anticipated to modulate the thermodynamics of amino acid radicals to achieve controlled, unidirectional PCET. Herein, square-wave voltammetry was employed to investigate the electrostatic effects on the redox properties of tryptophan in two variants of the protein azurin.

Multigenerational Theoretical Study of Isoprene Peroxy Radical 1-5-Hydrogen Shift Reactions that Regenerate HO Radicals and Produce Highly Oxidized Molecules.

A computational protocol is employed to glean new insight into the kinetics of several 1,5-hydrogen atom (H) shift reactions subsequent to first- and second-generation OH/O additions to isoprene. The M06-2X density functional was initially used with the Nudged Elastic Band (NEB) method to determine the potential energy surface of OH/O addition reactions, the 1,5-H shift reactions, and the fragmentation exit channels. The Master Equation Solver for Multi-Energy Well Reactions (MESMER) was applied to determine the rate constants for OH addition and the 1,5-H shifts.

Harmonizing accuracy and efficiency: A pragmatic approach to fragmentation of large molecules.

Fragmentation methods offer an attractive alternative for treatment of large molecules and molecular clusters. However, balancing the accuracy and efficiency of these methods is a tight-rope-act. With this in view, we present an algorithm for automatic molecular fragmentation within Molecular Tailoring Approach (MTA) achieving this delicate balance.

Noncovalent interactions underlying binary mixtures of amino acid based ionic liquids: insights from theory.

Mixtures of ionic liquids formed by blending a common 1-methyl-3-butylimidazolium [Bmim] cation with the dicarboxylic amino acid anions viz., aspartic acid [Asp], asparagine [Asn], glutamic acid [Glu], and glutamine [Gln], have been investigated by employing dispersion corrected density functional theory. Binary mixtures of [Bmim][Asp][Asn] and [Bmim][Glu][Gln] ionic liquids emerge with distinct structural patterns.

Barrierless Reactions with Loose Transition States Govern the Yields and Lifetimes of Organic Nitrates Derived from Isoprene.

The chemical reaction mechanism of NO addition to two β and δ isoprene hydroxy-peroxy radical isomers is examined in detail using density functional theory, coupled cluster methods, and the energy resolved master equation formalism to provide estimates of rate constants and organic nitrate yields. At the M06-2x/aug-cc-pVTZ level, the potential energy surfaces of NO reacting with β-(1,2)-HO-IsopOO and δ-Z-(1,4)-HO-IsopOO possess barrierless reactions that produce alkoxy radicals/NO and organic nitrates. The nudged elastic band method was used to discover a loosely bound van der Waals (vdW) complex between NO and the alkoxy radical that is present in both exit reaction channels.

Glycoconjugated Site-Selective DNA-Methylating Agent Targeting Glucose Transporters on Glioma Cells.

DNA-alkylating drugs continue to remain an important weapon in the arsenal against cancers. However, they typically suffer from several shortcomings because of the indiscriminate DNA damage that they cause and their inability to specifically target cancer cells. We have developed a strategy for overcoming the deficiencies in current DNA-alkylating chemotherapy drugs by designing a site-specific DNA-methylating agent that can target cancer cells because of its selective uptake via glucose transporters, which are overexpressed in most cancers.

Probing Molecular Interactions in Functionalized Asymmetric Quaternary Ammonium-Based Dicationic Ionic Liquids.

Electronic structure, binding energies, and spectral characteristics of functionalized asymmetric dicationic ionic liquids (DILs) composed of quaternary ammonium cations substituted with the ethoxyethyl and allyl/3-phenylpropyl/methoxyethoxyethyl/pentyl functionalities on two different nitrogen centers of the dication and the bis(trifluoromethanesulfonyl)imide (TfN) anion were derived employing the dispersion-corrected density functional theory. DILs based on methoxyethoxyethyl-substituted cation reveal stronger binding toward the TfN anion. The measured glass transition temperatures are found to be strongly dependent on the cation-anion binding facilitated through noncovalent interactions with dominant contributions from the electrostatics and hydrogen bonding.

Encaged molecules in external electric fields: A molecular "tug-of-war".

Response of polar molecules CH3OH and H2O2 and a non-polar molecule, CO2, as "guests" encapsulated in the dodecahedral water cage (H2O)20 "host," to an external, perturbative electric field is investigated theoretically. We employ the hybrid density-functionals M06-2X and ωB97X-D incorporating the effects of damped dispersion, in conjunction with the maug-cc-pVTZ basis set, amenable for a hydrogen bonding description. While the host cluster (cage) tends to confine the embedded guest molecule through cooperative hydrogen bonding, the applied electric field tends to rupture the cluster-composite by stretching it; these two competitive effects leading to a molecular "tug-of-war.

The N-terminal of annexin A1 as a secondary membrane binding site: a molecular dynamics study.

Annexin A1 has been shown to cause membrane aggregation and fusion, yet the mechanism of these activities is not clearly understood. In this work, molecular dynamics simulations were performed on monomeric annexin A1 positioned between two negatively charged monolayers using AMBER's all atom force field to gain insight into the mechanism of fusion. Each phospolipid monolayer was made up of 180 DOPC molecules and 45 DOPG molecules to achieve a 4:1 ratio.

A computational study of acid catalyzed aerosol reactions of atmospherically relevant epoxides.

Epoxides are important intermediates of atmospheric isoprene oxidation. Their subsequent reactions in the particle phase lead to the production of organic compounds detected in ambient aerosols. We apply density functional theory to determine the important kinetic factors that drive epoxide reactions in the particle phase.

Epoxide as a precursor to secondary organic aerosol formation from isoprene photooxidation in the presence of nitrogen oxides.

Isoprene is a substantial contributor to the global secondary organic aerosol (SOA) burden, with implications for public health and the climate system. The mechanism by which isoprene-derived SOA is formed and the influence of environmental conditions, however, remain unclear. We present evidence from controlled smog chamber experiments and field measurements that in the presence of high levels of nitrogen oxides (NO(x) = NO + NO2) typical of urban atmospheres, 2-methyloxirane-2-carboxylic acid (methacrylic acid epoxide, MAE) is a precursor to known isoprene-derived SOA tracers, and ultimately to SOA.

Exploring electric field induced structural evolution of water clusters, (H2O)n [n = 9-20]: density functional approach.

Response of neutral water clusters (H(2)O)(n), n = 9-20, to external uniform dipolar static electric fields is studied for some lowest-energy conformers for each "n" within an energy band of about 9 kcal mol(-1) of their field-free counterparts. We perform density functional theory computations with B3LYP∕6-311++G(2d,2p) model chemistry. Increasing the electric field destabilizes and distorts a cluster by elongating, hence weakening its hydrogen bonds, culminating into a catastrophic structural breakdown beyond a specific threshold field-strength.

Intramolecular hydrogen bond energy and cooperative interactions in α-, β-, and γ-cyclodextrin conformers.

Accurate estimation of individual intramolecular hydrogen bond (H-bond) energies is an intricate task for multiply H-bonded systems. In such cases, the hydrogen bond strengths could be highly influenced by the cooperative interactions, for example, those between hydroxyl groups in sugars. In this work, we use the recently proposed molecular tailoring approach-based quantification (Deshmukh, Gadre, and Bartolotti, J Phys Chem A 2006, 110, 12519) to the extended systems of cyclodextrins (CDs).

Microsolvation of methyl hydrogen peroxide: ab initio quantum chemical approach.

Methyl hydrogen peroxide (MHP), one of the simplest organic hydroperoxides, is a strong oxidant, with enhanced activity in aqueous ambience. The present study investigates, at the molecular level, the role of hydrogen bonding that is conducive to cluster formation of MHP with water molecules from its peroxide end, with the methyl group remaining hydrophobic for up to five water molecules. Ab initio quantum chemical computations on MHP.

Computational screening and design of S100B ligand to block S100B-p53 interaction.

The binding of S100B to p53 disables the biological function of p53 as a tumor suppressor and thus causes cancer. It is very important to explore the interaction between S100B and p53 and to develop inhibitors to block the interaction in anti-cancer development. In this work, the interaction of S100B to p53 was studied using molecular dynamics (MD) at the atomic level and organic molecules have been identified as potential inhibitors to block the S100B-p53 interaction.

Molecular dynamics simulation studies on Ca2+ -induced conformational changes of annexin I.

Cryo-electron microscopy (EM) and X-ray studies proposed different mechanisms for annexin-induced membrane aggregation. In this work, molecular dynamics (MD) simulation technique was utilized to gain an insight into the calcium-induced conformational changes on annexin I and their implication in membrane aggregation mechanism. MD simulations were performed on the Ca2+ -free annexin I with the N-terminal domain buried inside the core (System 1), the Ca2+ -bound annexin I without N-terminal domain (System 2) and the Ca2+ -bound annexin I with the N-terminal domain exposed (System 3).

Intramolecular hydrogen bonding and cooperative interactions in carbohydrates via the molecular tailoring approach.

In spite of many theoretical and experimental attempts for understanding intramolecular hydrogen bonding (H-bonding) in carbohydrates, a direct quantification of individual intramolecular H-bond energies and the cooperativity among the H-bonded networks has not been reported in the literature. The present work attempts, for the first time, a direct estimation of individual intramolecular O-H..

Copper and zinc promote interactions between membrane-anchored peptides of the metal binding domain of the prion protein.

The prion protein (PrP) has been identified as a metalloprotein capable of binding multiple copper ions and possibly zinc. Recent studies now indicate that prion self-recognition may be an important factor in both the normal function and misfunction of this protein. We have developed fluorescently labeled models of the prion protein that allow prion-prion interactions and metal binding to be investigated on the molecular level.

Density functional theory-based prediction of some aqueous-phase chemistry of superheavy element 111. Roentgenium(I) is the "softest" metal ion.

A previous approach (Hancock, R. D.; Bartolotti, L.

Estimation of intramolecular hydrogen bond energy via molecular tailoring approach.

A novel method, based on the molecular tailoring approach for estimating intramolecular hydrogen bond energies, is proposed. Here, as a case study, the O-H..

Interaction of peroxyformic acid with water molecules: a first-principles study.

The present article comprises a theoretical study of structures and energetics of the lowest energy conformers of peroxyformic acid (PFA) and its hydrated variants, viz. PFA..

Structures, energetics, and vibrational spectra of H2O2...(H2O)n, n = 1-6 clusters: Ab initio quantum chemical investigations.

Hydrogen-bonded heteroclusters of H(2)O(2)...

An example where orbital relaxation is an important contribution to the Fukui function.

Density-functional electronic structure calculations are performed on the molecules Cr2(hpp)4, Mo2(hpp)4, and W2(hpp)4, where the bridging ligand, hpp, is the anion of 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidine. The calculated electronic densities are used to determine the Fukui functions. These molecules are unique not only in their ability as electron donors but also because orbital relaxation plays a decisive role in their reactivity.