Molecular Energetics Research Articles

Prediction of halocarbon toxicity from structure: a hierarchical QSAR approach

Mathematical structural invariants and quantum theoretical descriptors have been used extensively in quantitative structure–activity relationships (QSARs) for the estimation of pharmaceutical activities, biological properties, physicochemical properties, and the toxicities of chemicals. Recently our research team has explored the relative importance of various levels of chemodescriptors, i.e. topostructural (TS), topochemical (TC), geometrical (3D), and quantum theoretical descriptors, in property estimation. This study examines the contribution of chemodescriptors ranging from topostructural to quantum theoretic calculations, up to the Gaussian STO-3G level, in predicting the results of six indicators of oxidative stress for a set of 20 halocarbons. Using quantum theoretical calculations in this study is of particular interest as molecular energetics is related to the likelihood of electron attachment and free radical formation, the mechanism of toxicity for these chemicals and should aid in modeling their potential for oxidative stress.

Millisecond pulsed radio frequency glow discharge time of flight mass spectrometry: temporal and spatial variations in molecular energetics

The internal energy distributions, P(ε), of a millisecond pulsed radio frequency glow discharge plasma were investigated using tungsten hexcarbonyl W(CO) 6 as a “thermometer molecule”. Vapor of the probe molecule, W(CO) 6, was introduced into the plasma and subjected to various ionization and excitation processes therein. The resultant molecular and fragment ions were monitored using a Time-of-Flight mass spectrometer. Ion abundance data were utilized in combination with the known energetics of W(CO) 6 to construct the P(ε) plots. The P(ε) of W(CO) 6 exhibited strong temporal dependence over the pulse cycle: Distinct internal energy distributions were found at the discharge breakdown period (prepeak), the steady state period (plateau), and the post-pulse period (afterpeak). Spatial variation in P(ε) was also observed, especially during the plateau regime. The observations suggest that this pulsed glow discharge affords excellent energy tunability that can be used to perform selective ionization and fragmentation for molecular, structural, and elemental information. Parametric studies were performed to evaluate the effects of discharge pressure and operating power on P(ε). These studies also provided insight into the correlation of the observed P(ε)s with the fundamental ionization and excitation mechanisms in the plasma. The temporal and spatial variations in P(ε) were hence attributed to changes in the dominant energy transfer processes at specific times in specific regions of the plasma. These data will be useful in future efforts to optimize the analytical performance of this source for chemical speciation.

Millisecond pulsed radio frequency glow discharge time of flight mass spectrometry: temporal and spatial variations in molecular energetics

Millisecond pulsed radio frequency glow discharge time of flight mass spectrometry: temporal and spatial variations in molecular energetics

An AM1 study on a certain cyclophane fused spirooxazine system and some of its isomers

A certain spirooxazine system containing azaindoline moiety as well as a cyclophane system has been considered. Also its isomeric forms, acyclic isomers, of the spirocompound have been the present concern for the AM1 (RHF) type semiempirical quantum-chemical treatment. Some geometrical and physicochemical data, thermodynamic as well as molecular orbital energetics and UV–Vis spectral characteristics have been presented.

Molecular structures and energetics of the neutral aluminum–trimethylaluminum complex: an Al–Al bonded global minimum?

From their recent laboratory kinetics studies, Parker and Nelson have proposed a monobridged molecular structure for the aluminum atom–trimethylaluminum system. Here molecular structures and energetics for the neutral aluminum atom–trimethylaluminum complex (AlTMA) are reported from theory. A second distinct minimum was located and characterized, corresponding to an unanticipated H 3C–Al–Al(CH 3) 2 geometry. In addition, the transition state between the two minima was located. The relative energies of these stationary points are also reported, predicting that the monobridged AlTMA structure recently reported is higher in energy than the methylaluminum DMA discovered in this study by about 2 kcal mol −1.

Molecular mechanics—modeling molecular structure and energetics: the 2002 Benjamin Franklin Medal in Chemistry presented to Norman Allinger

The Franklin Institute of Philadelphia awarded the 2002 Benjamin Franklin Medal in Chemistry to Norman L. Allinger for his pioneering work in computational chemistry in the field of molecular mechanics with his development of the MM series of force fields, their widespread application to the fundamental understanding of molecular structure and energetics, and their implementation as a significant tool to practicing chemists.

Synthesis, spectroscopy and structure of CF3CH2OCN, CF3CH2NCO, and (CF3CH2O)2CNHElectronic supplementary information (ESI) available: Experimental and calculated infrared and Raman vibrational frequencies and intensities of CF3CH2OCN, (CF3CH2O)2CNH and CF3CH2NCO. See http://www.rsc.org/suppdata/cp/b2/b212777f/

The reaction between BrCN and CF3CH2OH in the presence of Et3N has been investigated in acetone and ether solvents. Three different products have been isolated in the reaction, CF3CH2OCN (1), the novel molecule (CF3CH2O)2CNH (2), and Et2NCN. The product ratio is observed to depend strongly on (i) the solvent used, (ii) the ratio of the reagents, and (iii) the speed of the addition of Et3N to the reaction mixture. By varying these factors, either 1 or 2 can be obtained as the major reaction product. CF3CH2NCO (3) is generated in the gas phase by thermolysis of 2 and Ph2NC(O)NHCH2CF3 precursors. 1, 2, and 3 are characterized in the gas phase by infrared, 2 in the liquid state by Raman, and 1 and 2 in solution by NMR spectroscopies for the first time. The molecular geometries and energetics of the possible conformers are obtained from DFT calculations at the B3LYP level of theory. The observed vibrational frequencies are compared with the results of the DFT calculations, supporting the identification and assisting with the assignments.

Midinfrared and Quantum-Chemical Study of the Structure, Conformation, and Isomerization of the Unstable CH3CH2OCN Molecule

Gaseous ethyl cyanate, CH 3 CH 2 OCN, has been generated from the gas/solid reaction of O-ethyl thiocarbamate with mercury oxide and characterized in the gas phase by infrared spectroscopy for the first time. Experimental data indicate the presence of two conformers in the gas phase, the gauche (synclinal) and the trans (antiperiplanar) form. The molecular geometries and energetics of the possible conformers are obtained from DFT calculations at the B3LYP level and from ab initio calculations at the MP2, MP3, MP4, QCISD, and CCSD(T) levels of theory. The assignment of the gas-phase infrared spectrum is assisted by normal coordinate calculations based on the scaled computed force field of the two conformers. The kinetic instability of CH 3 -CH 2 OCN toward isomerization is studied at the B3LYP level, in a vacuum and in solutions. Solvent effects are modeled using the polarized continuum model (PCM). Calculations show that the isomerization is not a unimolecular process at ambient temperatures, and bimolecular processes are responsible for the instability. In polar solvents, the OCN - anion plays a key role in the isomerization, being an effective catalyst for the cyanate-isocyanate rearrangement.

Regularities in the bond dissociation enthalpies of molecules of types AB and BAB: Energetics of 10‐ and 16‐valence electron ions of groups 13, 15, and 16

AbstractFor the quantitative and qualitative understanding of molecular energetics, contemporary calorimetric and mass spectrometric measurement techniques and correspondingly high‐level quantum chemical calculational methodologies increasingly work in concert. For example, letting A and B be group 14 and 16 elements, respectively, for their 10‐valence electron AB and 16‐valence electron AB2 gas‐phase diatomic and triatomic species, the bond enthalpy ratio 〈D(AB2)〉/D(AB) has been shown to remarkably constant, namely, 0.77 ± 0.02. In the current study we discuss the corresponding bond enthalpy ratio for the valence isoelectronic cations and anions, e.g., for the carcinogen [NO]+, explosive precursor [NO2]+, and discrete (monomeric, i.e., nonsalt containing) anions [BO2]− and [AlO2]−. From a combination of results taken from archival literature measurements and new quantum chemical calculations reported in this article, again roughly constant ratios are found. Numerically, these ratios are 0.66 ± 0.03 and 0.86 ± 0.02 for cations and anions, respectively. That the ratios increase in the order cation < neutral < anion is also explained in our study. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003

Promise of Advances in Simulation Methods for Protein Crystallography: Implicit Solvent Models, Time-Averaging Refinement, and Quantum Mechanical Modeling

Publisher Summary The objective of crystallographic-refinement methods is to adjust atomic coordinates and other structural parameters of the molecular model to minimize disagreement between model and experimental data—namely, calculated and measured structure factors, F calc and F obs . This chapter describes three developments in the field of simulations of molecular energetics that have the potential to enhance crystallographic studies of a protein structure. First, the representation of salvation with an implicit solvent model should provide a significant improvement over current practice in energy-constrained refinement by allowing inclusion of a full set of long-range forces in a now-complete energy function. Second, time-averaging refinement offers unique opportunities for determining physically realistic dynamic side chain and solvent structure within the context of experimental data; that is, the structure factors. This technique is, however, limited to high-resolution data sets because of the need for a high parameter-to-unknown ratio. Third, the use of quantum mechanics to evaluate the molecular energy and forces holds promise for future refinements when applied wholesale but is already capable of producing valuable insights when applied to a structural detail.

A new model for simulating 3-d crystal growth and its application to the study of antifreeze proteins.

A novel computational technique for modeling crystal formation has been developed that combines three-dimensional (3-D) molecular representation and detailed energetics calculations of molecular mechanics techniques with the less-sophisticated probabilistic approach used by statistical techniques to study systems containing millions of molecules undergoing billions of interactions. Because our model incorporates both the structure of and the interaction energies between participating molecules, it enables the 3-D shape and surface properties of these molecules to directly affect crystal formation. This increase in model complexity has been achieved while simultaneously increasing the number of molecules in simulations by several orders of magnitude over previous statistical models. We have applied this technique to study the inhibitory effects of antifreeze proteins (AFPs) on ice-crystal formation. Modeling involving both fish and insect AFPs has produced results consistent with experimental observations, including the replication of ice-etching patterns, ice-growth inhibition, and specific AFP-induced ice morphologies. Our work suggests that the degree of AFP activity results more from AFP ice-binding orientation than from AFP ice-binding strength. This technique could readily be adapted to study other crystal and crystal inhibitor systems, or to study other noncrystal systems that exhibit regularity in the structuring of their component molecules, such as those associated with the new nanotechnologies.

Molecular Structure, Vibrational Frequencies, and Energetics of the HCO, HOCO, and HCO2 Anions

The structures and vibrational spectra for HCO-, HOCO- and HCO2- have been calculated at high levels of electronic structure theory. The changes in the structure of HCO- relative to neutral HCO are consistent with the predictions from photodetachment experiments. Of the two isomers, HCO2- and HOCO-, the HCO2- anion is predicted to be the more stable. For HOCO-, the cis conformer of lower energy as compared to the trans. Conversely, for neutral HOCO, the trans conformer is lower in energy. The electron affinity of HCO is predicted to be 0.308 eV in excellent agreement with the experimental value of 0.313 eV. The electron affinity of HOCO is predicted to be 1.42 eV and there is no known experimental measurement. The electron affinity of HCO2(2A1) is predicted to be 3.51 eV as compared to the experimental value of 3.498+ 0.015 eV. The 2A1 state of HCO2 is predicted to be the ground state on the basis of theoretical calculations, which are in agreement with the experimental assignment determined from the photoelectron spectra.

Molecular Structures and Electron Affinities for the Chlorine Oxides ClOO, ClOOO, and ClO3(C3v)

The molecular structures and energetics of ClOO, ClOOO, and ClO3 (C3v) have been studied using four independent density functional theory methods. The methods used have been carefully calibrated against a comprehensive tabulation of experimental electron affinities (Chem. Rev. 2002, 102, 231). Optimized geometries, adiabatic electron affinities, vertical electron affinities, and vertical detachment energies are reported. Vibrational frequencies and bond dissociation energies are also reported. These density functional theory methods were utilized in conjunction with the double-ζ plus polarization basis set augmented with diffuse s-type and p-type functions (DZP++). Among these, the unrestricted BHLYP and B3LYP methods used for the open-shell ClOO and ClOOO systems lead to serious spin contamination, while the BLYP and BP86 methods have relatively little spin contamination (〈S2〉 < 0.76). The reliable predicted adiabatic electron affinities with the BLYP functional are 3.33 (ClOO), 3.97 (ClO3), and 2.84 (ClOOO) eV. The electronic ground state of ClOO- is a triplet (3A‘ ‘) state. There are seven local minima on the potential energy surface for ClOOO-; among them the gauche structure is the global minimum. The ClOO- and ClOOO- ground states may be regarded as Cl-···O2 and Cl-···O3 complexes, respectively. The ClOO- anion triplet state is predicted to lie 49−52 kcal/mol below OClO-. The neutral ClOOO isomer is predicted to lie 57 kcal/mol below the C3v structure ClO3. gauche-ClOOO- is predicted to lie 31 kcal/mol (BLYP) below the ClO3- (C3v) structure.

Coordination of {Ru II(NO +)} 3+ and {Ru II(H 2O)} 2+ to bleomycin: most favored [Ru II(L)(BLM-A 2)] structure according to 1H NMR and molecular mechanics methods

The {Ru II(NO) +} 3+ derivatives of bleomycin-A 2 and bleomycin-B 2 have been prepared from the reaction of Ru(NO)Cl 3(H 2O) 2 with the commercially available Blenoxane antitumor agent. The coordination identity of the BLM donor groups in [RuNO)(BLM's)] was established using 500 MHz 1H NMR spectral studies as the histidine imidazole, deprotonated histidyl amide, the pyrimidyl nitrogen, the secondary amine and the terminal β-aminoalanine functionalities as proposed previously for Fe II(BLM), ‘active Fe(BLM)’, Co III(BLM), and Cu II(BLM) by various other investigators. Equivalent chemical shifts for the donors and adjacent protons of the metal binding region support the same coordination of both the A 2 and B 2 forms at the metal-binding domain. Molecular mechanics calculations were carried out for the dominant [Ru II(L)(BLM-A 2)] complex, L=NO + and H 2O, using mmff94 software for 15 different structures that include all the possible screw-sense isomers that involve the stereochemical placement of the bithiazole binding tail and the mannose sugar region of BLM. These calculations determined the R, R-sp-1 structure of [Ru II(NO +)(BLM-A 2)] to be of lowest energy, the opposite chirality from that proposed by Stubbe, Kozarich and co-workers for the stereochemistry of [Co III(BLM-A 2)(OOH −)] and [Co III(BLM-A 2)(H 2O)]. The R, R-sp-1 structure places the bithiazole tail near the axial β-aminoalanine amine donor, and the mannose sugar region near the axial NO + chromophore, but not at an H-bonded distance. The R, R-sp-1 structure as indicated for the lowest energy form by mmff94 for [Ru(NO)(BLM-A 2)] is also indicated as the one present at 25 °C in D 2O solution by the 1H NMR spectra. Of the commonly suggested structures for M(BLM's), the mmff94 calculations for [Ru II(NO +)(BLM-A 2)] agree with Zimmer's former findings using Monte Carlo methods for the R, R screw-sense isomer as being lowest in energy for [Co III(BLM-A 2)(OOH −)], and gave a stability order of the various proposed M(BLM) structures for [Ru(NO)(BLM-A 2's)] as R, R-sp-1> R, R-sp basket (after Marzilli et al.)>Stubbe et al.'s R, R> S, S-sp basket> S, S-sp-1>Stubbe et al.'s S, S>OP (after Oppenheimer–Hecht) structures. The presence of a coordinated H 2O ligand instead of NO + changes the strain, raising the energies of the complexes relative to their nitrosyl analogues. The energy-minimized structures show that depending upon the chirality of the species, either the bithiazole or the sugar pendant arm approaches near (within ca. 2.0–2.5 A) of the water ligand, establishing an H-bonded association with the coordinated H 2O. This interaction alters the relative order of structural stabilities, and makes the energies of the several structural forms more nearly comparable. The mmff94 stability order as calculated for [Ru II(H 2O)(BLM-A 2)] is observed to be R, R-sp∼ S, S-sp∼Stubbe S, S∼ R, R-sp-1(all with very similar energies)> S, S-sp-1>Stubbe R, R≫OP. Therefore, having an H-bondable axial ligand such as H 2O or O 2H − makes all structural forms, except for the OP structure, more comparable in energy. Among these, a structure of R, R chirality is modestly favored, although the Stubbe S, S approaches very comparable molecular mechanics energetics to that of R, R-sp or R, R-sp-1. The present work emphasizes the delicate balance in favored M(L)(BLM) structures, and that order of these are a function of the nature of the axial ligand L and the metal center chosen for study. Therefore, conclusions as to the structures of metallo-bleomycins that are drawn from data taken from ‘inert’, non-H-bonding axial ligands such as CO may not be transferable to complexes that possess H-bondable axial ligands.

Analysis of non-planar graphitic structures: from arched edge planes of graphite crystals to nanotubes

A unified approach to the analysis of the mechanisms that lead to the edge reconstruction of graphite and growth of a variety of non-planar graphitic structures, such as nanotubes, is suggested. Transmission electron microscopy (TEM) shows that nano-arches are formed on the edge planes of natural and synthetic graphite, as well as graphite polyhedral crystals, which are built of graphene sheets; this makes the edge reconstruction of graphite different from the surface reconstruction of other crystals. A theoretical study of edge zipping in graphite and formation of tubular carbon structures has been performed using an integrated approach combining molecular dynamics simulation and analytical continual energetics modeling. The suggested theoretical framework describes the formation of curved surfaces in a wide range of dimensions, which is a general feature of the growth of layered materials. Layered materials isostructural to graphite, such as hexagonal BN, demonstrate similar edge structures and also form nanotubes. Thus, the ability of materials to form arches as a result of edge reconstruction points out to their ability to form nanotubes and vice versa. TEM studies of graphite and hexagonal boron nitride provide experimental verification of our analytical model.

An ab initio/Rice–Ramsperger–Kassel–Marcus study of photodissociation of carbonyl cyanide

AbstractThe geometries and vibrational frequencies of the parent molecule, intermediates, transition state, and products involved in the photochemical decay of carbonyl cyanide NC–C(O)–CN have been studied by ab initio calculations at the MP2/6‐311G* level. The energies of various species have been refined using the modified Gaussian‐2 [G2M(MP2)] method. The molecular parameters and energetics derived from the ab initio calculations were used to compute microcanonical rate constants of all possible reaction steps of photodissociation of the carbonyl cyanide employing the conventional and variational RRKM theory and to obtain the product branching ratios. The results show that the radical decay, CO(CN)2+ hν→OCCN/OCNC+CN, is dominant (86.14% and 13.85% for OCCN and OCNC, respectively), while the molecular decay, CO(CN)2→CO+NCCN, gives only a trace amount of the products. Whereas the computed radical product yields qualitatively agree with those measured in experiment (Scheld, H. A., et al. J Chem Phys 1999, 111, 923), the calculated branching ratio for the molecular decay channel underestimates the experimental value of ∼6%. This deviation may be attributed to the deficiencies in the variational RRKM treatment of the radical decay rate constants and/or to some nonstatistical behavior of the system which enhances the molecular decay. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

Natural J-coupling analysis: interpretation of scalar J-couplings in terms of natural bond orbitals.

The natural J-coupling (NJC) method presented here analyzes the Fermi contact portion of J-coupling in the framework of finite perturbation theory applied to ab initio/density function theory (DFT) wave functions, to compute individual and pairwise orbital contributions to the net J-coupling. The approach is based on the concepts and formalisms of natural bond orbital (NBO) methods. Computed coupling contributions can be classified as Lewis (individual orbital contributions corresponding to the natural Lewis structure of the molecule), delocalization (resulting from pairwise donor-acceptor interactions), and residual repolarization (corresponding to correlation-like interactions). This approach is illustrated by an analysis of the angular and distance dependences of the contributions to vicinal (3)J(HH) couplings in ethane and to the long-range (6)J(HH) couplings in pentane. The results indicate that approximately 70% or more of the net J-coupling is propagated by steric exchange antisymmetry interactions between Lewis orbitals (predominantly sigma bonding orbitals). Hyperconjugative sigma to sigma delocalization interactions account for the remainder of the coupling. Calculated pairwise-steric and hyperconjugative-delocalization energies provide a means for relating coupling mechanisms to molecular energetics. In this way, J-coupling contributions can be related directly to the localized features of the molecular electronic structure in order to explain measured J-coupling patterns and to predict J-coupling trends that have yet to be measured.

Computational study of dimethyl‐ and trimethyl‐tin(IV) complexes of porphyrin derivatives

AbstractThe molecular geometry, energetics and electronic charge distribution of diorgano‐ and triorgano‐tin(IV) complexes of [protoporphyrin‐IX] and [meso‐tetra(4‐carboxyphenyl)porphine] derivatives were determined at semi‐empirical and ab initio levels. To study the molecular details of the complexes, simpler molecule models were calculated by the ab initio pseudo‐potential method. The molecular properties of these complexes are essentially independent of the presence of the peripheral tin atoms. Agreement was always found among the results of the different computational approaches, as well as between the theoretical and the experimental findings on the molecular geometry of the hypothesized complexes. Interaction modes between water and the organo‐tin systems considered were affected strongly by the presence of peripheral tin atoms. Copyright © 2001 John Wiley &amp; Sons, Ltd.

Ab Initio Study of the Adamantonium Cations: the Protonated Adamantane

The molecular structure and energetics of the adamantonium ions were computed at the MP2(full)/6-31G** level. Three structures were found to represent the adamantonium cations, respectively: the 1-H-adamantonium (1), 2-H-adamantonium (2), and C-adamantonium ions (3). This study revealed that, upon protonation, adamantane can also produce two van der Waals complexes: one formed by the weak interaction of the 1-adamantyl cation and H2 (4) and the other formed by the interaction of the 2-adamantyl cation and H2 (5). The stability order is predicted to be 5 > 3 > 4 > 1 > 2. Given the size and complexity of this molecule, the quantum zero point energy (ZPE) and finite temperature (298 K) corrections were estimated from previously calculated values for the isobutonium (for protonation of tertiary C−H and C−C bonds) and the proponium cations (for protonation of the secondary C−H bond). The calculated proton affinity of adamantane was estimated as 175.7 kcal/mol.

Nonadiabatic Multielectron Dynamics in Strong Field Molecular Ionization.

We report the observation of a general strong field ionization mechanism due to highly nonadiabatic multielectron excitation dynamics in polyatomic molecules. We observe that such excitation mechanisms greatly affect molecular ionization, fragmentation, and energetics. We characterized this phenomenon as a function of optical frequency, intensity, and molecular properties.