Showing papers in "Journal of Physical Chemistry A in 2007"

An Evaluation of Harmonic Vibrational Frequency Scale Factors

Abstract: Scale factors for obtaining fundamental vibrational frequencies, low-frequency vibrational frequencies, zeropoint vibrational energies (ZPVEs), and thermal contributions to enthalpy and entropy have been derived through a least-squares approach from harmonic frequencies determined at more than 100 levels of theory. Wave function procedures (HF, MP2, QCISD, QCISD(T), CCSD, and CCSD(T)) and a large and representative range of density functional theory (DFT) approaches (B3-LYP, BMK, EDF2, M05-2X, MPWB1K, O3-LYP, PBE, TPSS, etc.) have been examined in conjunction with basis sets such as 6-31G(d), 6-31+G(d,p), 6-31G(2df,p), 6-311+G(d,p), and 6-311+G(2df,p). The vibrational frequency scale factors were determined by a comparison of theoretical harmonic frequencies with the corresponding experimental fundamentals utilizing a standard set of 1066 individual vibrations. ZPVE scale factors were generally obtained from a comparison of the computed ZPVEs with experimental ZPVEs for a smaller standard set of 39 molecules, though the effect of expansion to a 48 molecule data set was also examined. In addition to evaluating the scale factors for a wide range of levels of theory, we have also probed the effect on scale factors of varying the percentage of incorporated exact exchange in hybrid DFT calculations using a modified B3-LYP functional. This has revealed a near-linear relationship between the magnitude of the scale factor and the proportion of exact exchange. Finally, we have investigated the effect of basis set size on HF, MP2, B3-LYP, and BMK scale factors by deriving values with basis sets ranging from 6-31G(d) up to 6-311++G(3df,3pd) as well as with basis sets in the cc-pVnZ and aug-cc-pVnZ series and with the TZV2P basis.

DFTB+, a sparse matrix-based implementation of the DFTB method.

Abstract: A new Fortran 95 implementation of the DFTB (density functional-based tight binding) method has been developed, where the sparsity of the DFTB system of equations has been exploited. Conventional dense algebra is used only to evaluate the eigenproblems of the system and long-range Coulombic terms, but drop-in O(N) or O(N2) modules are planned to replace the small code sections that these entail. The developed sparse storage structure is discussed in detail, and a short overview of other features of the new code is given.

General performance of density functionals.

Abstract: The density functional theory (DFT) foundations date from the 1920s with the work of Thomas and Fermi, but it was after the work of Hohenberg, Kohn, and Sham in the 1960s, and particularly with the appearance of the B3LYP functional in the early 1990s, that the widespread application of DFT has become a reality. DFT is less computationally demanding than other computational methods with a similar accuracy, being able to include electron correlation in the calculations at a fraction of time of post-Hartree-Fock methodologies. In this review we provide a brief outline of the density functional theory and of the historic development of the field, focusing later on the several types of density functionals currently available, and finishing with a detailed analysis of the performance of DFT across a wide range of chemical properties and system types, reviewed from the most recent benchmarking studies, which encompass several well-established density functionals together with the most recent efforts in the field. Globally, an overall picture of the level of performance of the plethora of currently available density functionals for each chemical property is drawn, with particular attention being dedicated to the relative performance of the popular B3LYP density functional.

Comparison of DFT Methods for Molecular Orbital Eigenvalue Calculations

Abstract: We report how closely the Kohn−Sham highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) eigenvalues of 11 density functional theory (DFT) functionals, respectively, correspond to the negative ionization potentials (−IPs) and electron affinities (EAs) of a test set of molecules. We also report how accurately the HOMO−LUMO gaps of these methods predict the lowest excitation energies using both time-independent and time-dependent DFT (TD−DFT). The 11 DFT functionals include the local spin density approximation (LSDA), five generalized gradient approximation (GGA) functionals, three hybrid GGA functionals, one hybrid functional, and one hybrid meta GGA functional. We find that the HOMO eigenvalues predicted by KMLYP, BH&HLYP, B3LYP, PW91, PBE, and BLYP predict the −IPs with average absolute errors of 0.73, 1.48, 3.10, 4.27, 4.33, and 4.41 eV, respectively. The LUMOs of all functionals fail to accurately predict the EAs. Although the GGA functionals inaccurately predict bot...

Understanding of assembly phenomena by aromatic-aromatic interactions: benzene dimer and the substituted systems.

Abstract: Interactions involving aromatic rings are important in molecular/biomolecular assembly and engineering. As a consequence, there have been a number of investigations on dimers involving benzene or other substituted π systems. In this Feature Article, we examine the relevance of the magnitudes of their attractive and repulsive interaction energy components in governing the geometries of several π−π systems. The geometries and the associated binding energies were evaluated at the complete basis set (CBS) limit of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using a least biased scheme for the given data set. The results for the benzene dimer indicate that the floppy T-shaped structure (center-to-center distance: 4.96 A, with an axial benzene off-centered above the facial benzene) is isoenergetic in zero-point-energy (ZPE) corrected binding energy (D0) to the displaced-stacked structure (vertical interplanar distance: 3.54 A). However, the T-shaped structure i...

Early Time Hydrogen-Bonding Dynamics of Photoexcited Coumarin 102 in Hydrogen-Donating Solvents: Theoretical Study

Abstract: To study the early time hydrogen-bonding dynamics of chromophore in hydrogen-donating solvents upon photoexcitation, the infrared spectra of the hydrogen-bonded solute-solvent complexes in electronically excited states have been calculated using the time-dependent density functional theory (TDDFT) method. The hydrogen-bonding dynamics in electronically excited states can be widely monitored by the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds. In this study, we have demonstrated that the intermolecular hydrogen bonds between coumarin 102 (C102) and hydrogen-donating solvents are strengthened in the early time of photoexcitation to the electronically excited state by theoretically monitoring the stretching modes of C=O and H-O groups. This is significantly contrasted with the ultrafast hydrogen bond cleavage taking place within a 200-fs time scale upon electronic excitation, proposed in many femtosecond time-resolved vibrational spectroscopy experiments. The transient hydrogen bond strengthening behaviors in excited states of chromophores in hydrogen-donating solvents, which we have demonstrated here for the first time, may take place widely in many other systems in solution and are very important to explain the fluorescence-quenching phenomena associated with some radiationless deactivation processes, for example, the ultrafast solute-solvent intermolecular electron transfer and the internal conversion process from the fluorescent state to the ground state.

Extending the Power of Quantum Chemistry to Large Systems with the Fragment Molecular Orbital Method

Abstract: Following the brief review of the modern fragment-based methods and other approaches to perform quantum-mechanical calculations of large systems, the theoretical development of the fragment molecular orbital method (FMO) is covered in detail, with the emphasis on the physical properties, which can be computed with FMO. The FMO-based polarizable continuum model (PCM) for treating the solvent effects in large systems and the pair interaction energy decomposition analysis (PIEDA) are described in some detail, and a range of applications of FMO to biological studies is introduced. The factors determining the relative stability of polypeptide conformers (α-helix, β-turn, and extended form) are elucidated using FMO/PCM and PIEDA, and the interactions in the Trp-cage miniprotein construct (PDB: 1L2Y) are analyzed using PIEDA.

Electronic Structure and Bonding in Actinyl Ions and their Analogs

Abstract: This Feature Article seeks to present the current state of knowledge, both experimental and theoretical, of the electronic structure and bonding in actinyl ions and related species, such as the isoelectronic imido compounds as well as in linear triatomic actinide molecules of the type X-An-Y.

Unravelling the origin of intermolecular interactions using absolutely localized molecular orbitals.

Abstract: An energy decomposition analysis (EDA) method is proposed to isolate physically relevant components of the total intermolecular interaction energies such as the contribution from interacting frozen monomer densities, the energy lowering due to polarization of the densities, and the further energy lowering due to charge-transfer effects. This method is conceptually similar to existing EDA methods such as Morokuma analysis but includes several important new features. The first is a fully self-consistent treatment of the energy lowering due to polarization, which is evaluated by a self-consistent field calculation in which the molecular orbital coefficients are constrained to be block-diagonal (absolutely localized) in the interacting molecules to prohibit charge transfer. The second new feature is the ability to separate forward and back-donation in the charge-transfer energy term using a perturbative approximation starting from the optimized block-diagonal reference. The newly proposed EDA method is used to understand the fundamental aspects of intermolecular interactions such as the degree of covalency in the hydrogen bonding in water and the contributions of forward and back-donation in synergic bonding in metal complexes. Additionally, it is demonstrated that this method can be used to identify the factors controlling the interaction of the molecular hydrogen with open metal centers in potential hydrogen storage materials and the interaction of methane with rhenium complexes.

Electrodonating and electroaccepting powers.

Abstract: By introducing an electron bath that represents the chemical environment in which a chemical species is immersed, and by making use of the second-order Taylor series expansions of the energy as a function of the number of electrons in the intervals between N - 1 and N, and N and N + 1, we show that the electrodonating (omega-) and the electroaccepting (omega+) powers may be defined as omega-/+ = (mu-/+)2/2eta-/+, where mu-/+ are the chemical potentials and eta-/+ are the chemical hardnesses, in their corresponding intervals. Approximate expressions for omega- and omega+ in terms of the ionization potential I and the electron affinity A are established by assuming that eta- = eta+ = eta = mu+ - mu-. The functions omega-/+(r) = omega-/+f -/+(r), where f -/+(r) are the directional Fukui functions, derived from a functional Taylor series for the energy functional truncated at second order, represent the local electrodonating and electroaccepting powers.

Electrophilicity-based charge transfer descriptor.

Abstract: In line with the charge transfer (ΔNmax = −μ/η) proposed by Parr et al (Parr, R G; Szentpaly, L V; Liu, S J Am Chem Soc 1999, 121, 1922), we propose an electrophilicity-based charge transfer (ECT) descriptor in this paper and validate it through the interaction between a series of chlorophenols and DNA bases Application of ECT can be extended to the interaction of any toxin with the biosystem

Ultrafast hydrogen bond strengthening of the photoexcited fluorenone in alcohols for facilitating the fluorescence quenching.

Abstract: The time-dependent density functional theory (TDDFT) method was performed to investigate the excited-state hydrogen-bonding dynamics of fluorenone (FN) in hydrogen donating methanol (MeOH) solvent. The infrared spectra of the hydrogen-bonded FN-MeOH complex in both the ground state and the electronically excited states are calculated using the TDDFT method, since the ultrafast hydrogen-bonding dynamics can be investigated by monitoring the vibrational absorption spectra of some hydrogen-bonded groups in different electronic states. We demonstrated that the intermolecular hydrogen bond C=O...H-O between fluorenone and methanol molecules is significantly strengthened in the electronically excited-state upon photoexcitation of the hydrogen-bonded FM-MeOH complex. The hydrogen bond strengthening in electronically excited states can be used to explain well all the spectral features of fluorenone chromophore in alcoholic solvents. Furthermore, the radiationless deactivation via internal conversion (IC) can be facilitated by the hydrogen bond strengthening in the excited state. At the same time, quantum yields of the excited-state deactivation via fluorescence are correspondingly decreased. Therefore, the total fluorescence of fluorenone in polar protic solvents can be drastically quenched by hydrogen bonding.

Ab Initio Molecular Dynamics and Time-Resolved Photoelectron Spectroscopy of Electronically Excited Uracil and Thymine

Abstract: The reaction dynamics of excited electronic states in nucleic acid bases is a key process in DNA photodamage. Recent ultrafast spectroscopy experiments have shown multicomponent decays of excited uracil and thymine, tentatively assigned to nonadiabatic transitions involving multiple electronic states. Using both quantum chemistry and first principles quantum molecular dynamics methods we show that a true minimum on the bright S2 electronic state is responsible for the first step that occurs on a femtosecond time scale. Thus the observed femtosecond decay does not correspond to surface crossing as previously thought. We suggest that subsequent barrier crossing to the minimal energy S2/S1 conical intersection is responsible for the picosecond decay.

Rapid and Accurate Estimation of Densities of Room-Temperature Ionic Liquids and Salts

Abstract: Volume parameters for room-temperature ionic liquids (RTILs) and salts were developed. For 59 of the most common imidazolium, pyridinium, pyrrolidinium, tetralkylammonium, and phosphonium-based RTILs, the mean absolute deviation (MAD) of the densities is 0.007 g cm-3; for 35 imidazolium-based room-temperature salts, the MAD is 0.020 g cm-3; and for 150 energetic salts, the MAD is 0.035 g cm-3. The experimental density (Y) for an alkylated imidazolium or pyridinium-based room-temperature ionic liquid is approximately proportional to its calculated density (X) in the solid state: Y = 0.948X − 0.110 (correlation coefficient: R2 = 0.998, for BF4-, PF6-, NTf2--containing ionic liquids); Y = 0.934X − 0.070 (correlation coefficient: R2 = 0.999, for OTf -, CF3CO2-, N(CN)2--containing ionic liquids).

Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method: Third-Order Expansion of the Density Functional Theory Total Energy and Introduction of a Modified Effective Coulomb Interaction

Abstract: The standard self-consistent-charge density-functional-tight-binding (SCC-DFTB) method (Phys. Rev. B 1998, 58, 7260) is derived by a second-order expansion of the density functional theory total energy expression, followed by an approximation of the charge density fluctuations by charge monopoles and an effective damped Coulomb interaction between the atomic net charges. The central assumptions behind this effective charge−charge interaction are the inverse relation of atomic size and chemical hardness and the use of a fixed chemical hardness parameter independent of the atomic charge state. While these approximations seem to be unproblematic for many covalently bound systems, they are quantitatively insufficient for hydrogen-bonding interactions and (anionic) molecules with localized net charges. Here, we present an extension of the SCC-DFTB method to incorporate third-order terms in the charge density fluctuations, leading to chemical hardness parameters that are dependent on the atomic charge state and...

Generalized energy-based fragmentation approach for computing the ground-state energies and properties of large molecules.

Abstract: We present a generalized energy-based fragmentation (GEBF) approach for approximately predicting the ground-state energies and molecular properties of large molecules, especially those charged and polar molecules. In this approach, the total energy (or properties) of a large molecule can be approximately obtained from energy (or properties) calculations on various small subsystems, each of which is constructed to contain a certain fragment and its local surroundings within a given distance. In the quantum chemistry calculation of a given subsystem, those distant atoms (outside this subsystem) are modeled as background point charges at the corresponding nuclear centers. This treatment allows long-range electrostatic interaction and polarization effects between distant fragments to be taken into account approximately, which are very important for polar and charged molecules. We also propose a new fragmentation scheme for constructing subsystems. Our test calculations at the Hartree-Fock and second-order Moller-Plesser perturbation theory levels demonstrate that the approach could yield satisfactory ground-state energies, the dipole moments, and static polarizabilities for polar and charged molecules such as water clusters and proteins.

The current state of ab initio calculations of optical rotation and electronic circular dichroism spectra.

Abstract: The current ability of ab initio models to compute chiroptical properties such as optical rotatory dispersion and electronic circular dichroism spectra is reviewed. Comparison between coupled cluster linear response theory and experimental data (both gas and liquid phase) yields encouraging results for small to medium-sized chiral molecules including rigid species such as (S)-2-chloropropionitrile and (P)-[4]triangulane, as well as conformationally flexible molecules such as (R)-epichlorohydrin. More problematic comparisons are offered by (S)-methyloxirane, (S)-methylthiirane, and (1S,4S)-norbornenone, for which the comparison between theory and experiment is much poorer. The impact of basis-set incompleteness, electron correlation, zero-point vibration, and temperature are discussed. In addition, future prospects and obstacles for the development of efficient and reliable quantum chemical models of optical activity are discussed, including the problem of gauge invariance, scaling of the coupled cluster approach with system size, and solvation.

Strategies to improve photostabilities in ultrasensitive fluorescence spectroscopy.

Abstract: Given the particular importance of dye photostability for single-molecule and fluorescence fluctuation spectroscopy investigations, refined strategies were explored for how to chemically retard dye photobleaching. These strategies will be useful for fluorescence correlation spectroscopy (FCS), fluorescence-based confocal single-molecule detection (SMD) and related techniques. In particular, the effects on the addition of two main categories of antifading compounds, antioxidants (n-propyl gallate, nPG, ascorbic acid, AA) and triplet state quenchers (mercaptoethylamine, MEA, cyclo-octatetraene, COT), were investigated, and the relevant rate parameters involved were determined for the dye Rhodamine 6G. Addition of each of the compound categories resulted in significant improvements in the fluorescence brightness of the monitored fluorescent molecules in FCS measurements. For antioxidants, we identify the balance between reduction of photoionized fluorophores on the one hand and that of intact fluorophores on the other as an important guideline for what concentrations to be added for optimal fluorescence generation in FCS and SMD experiments. For nPG/AA, this optimal concentration was found to be in the lower micromolar range, which is considerably less than what has previously been suggested. Also, for MEA, which is a compound known as a triplet state quencher, it is eventually its antioxidative properties and the balance between reduction of fluorophore cation radicals and that of intact fluorophores that defines the optimal added concentration. Interestingly, in this optimal concentration range the triplet state quenching is still far from sufficient to fully minimize the triplet populations. We identify photoionization as the main mechanism of photobleaching within typical transit times of fluorescent molecules through the detection volume in a confocal FCS or SMD instrument (<1-20 ms), and demonstrate its generation via both one- and multistep excitation processes. Apart from reflecting a major pathway for photobleaching, our results also suggest the exploitation of the photoinduced ionization and the subsequent reduction by antioxidants for biomolecular monitoring purposes and as a possible switching mechanism with applications in high-resolution microscopy.

Tight-binding density functional theory: an approximate Kohn-Sham DFT scheme

Abstract: The DFTB method is an approximate KS-DFT scheme with an LCAO representation of the KS orbitals, which can be derived within a variational treatment of an approximate KS energy functional. But it may also be related to cellular Wigner-Seitz methods and to the Harris functional. It is an approximate method, but it avoids any empirical parametrization by calculating the Hamiltonian and overlap matrices out of DFT-derived local orbitals (atomic orbitals, AO's). The method includes ab initio concepts in relating the Kohn-Sham orbitals of the atomic configuration to a minimal basis of the localized atomic valence orbitals of the atoms. Consistent with this approximation, the Hamiltonian matrix elements can strictly be restricted to a two-center representation. Taking advantage of the compensation of the so-called "double counting terms" and the nuclear repulsion energy in the DFT total energy expression, the energy may be approximated as a sum of the occupied KS single-particle energies and a repulsive energy, which can be obtained from DFT calculations in properly chosen reference systems. This relates the method to common standard "tight-binding" (TB) schemes, as they are well-known in solid-state physics. This approach defines the density-functional tight-binding (DFTB) method in its original (non-self-consistent) version.

Block-localized wavefunction (BLW) method at the density functional theory (DFT) level.

Abstract: The block-localized wavefunction (BLW) approach is an ab initio valence bond (VB) method incorporating the efficiency of molecular orbital (MO) theory. It can generate the wavefunction for a resonance structure or diabatic state self-consistently by partitioning the overall electrons and primitive orbitals into several subgroups and expanding each block-localized molecular orbital in only one subspace. Although block-localized molecular orbitals in the same subspace are constrained to be orthogonal (a feature of MO theory), orbitals between different subspaces are generally nonorthogonal (a feature of VB theory). The BLW method is particularly useful in the quantification of the electron delocalization (resonance) effect within a molecule and the charge-transfer effect between molecules. In this paper, we extend the BLW method to the density functional theory (DFT) level and implement the BLW-DFT method to the quantum mechanical software GAMESS. Test applications to the π conjugation in the planar allyl r...

Application of density functional theory and vibrational spectroscopy toward the rational design of ionic liquids.

Abstract: D. functional theory methods in combination with vibrational spectroscopy are used to investigate possible variants of mol. structure of the ion pairs of several imidazolium-based ionic liqs. (ILs). Multiple stable structures are detd. with the anion positioned (a) near to the C2 atom of the imidazolium ring, (b) between N1 and C5, (c) between N3 and C4, and (d) between C4 and C5. Chloride and bromide anions in vacuum also occupy positions above or below the imidazolium ring, but in the condensed state these positions are destabilized. In comparison with the halides that almost equally occupy the positions (a-d), tetrafluoroborate and hexafluorophosphate anions strongly prefer position (a). The position and the type of the anion influence the conformation of the side chains bound to the imidazolium N1 atom, which are able to adopt in vacuum all usual staggered or eclipsed conformations, although in the liq. state some of the conformations are present only as minor forms if at all. Vibrations of the cations depend both on the conformational changes and on the assocn. with the anion. The formation of the ion pairs influences mainly stretching and out-of-plane vibrations of the imidazolium C-H groups and stretching vibrations of the perfluoroanions. Other modes of the ions retain their individuality and practically do not mix. This allows "interionic" vibrations to be sepd. and to regard the couple of the ions as an anharmonic oscillator. Such a model correlates the mol. structure of various ILs and their m.ps. without involving the energy of the interaction between the cations and anions but explains structure-m.p. correlations on the grounds of quasy-elastic properties.

Computational Studies of the Photophysics of Hydrogen-Bonded Molecular Systems

Abstract: The role of electron- and proton-transfer processes in the photophysics of hydrogen-bonded molecular systems has been investigated with ab initio electronic-structure calculations. Adopting indole, pyridine, and ammonia as molecular building blocks, we discuss generic mechanisms of the photophysics of isolated aromatic chromophores (indole), complexes of π systems with solvent molecules (indole−ammonia, pyridine−ammonia), hydrogen-bonded aromatic pairs (indole−pyridine), and intramolecularly hydrogen-bonded π systems (7-(2‘-pyridyl)indole). The reaction mechanisms are discussed in terms of excited-state minimum-energy paths, conical intersections, and the properties of frontier orbitals. A common feature of the photochemistry of the various systems is the electron-driven proton-transfer (EDPT) mechanism: highly polar charge-transfer states of 1ππ*, 1nπ*, or 1πσ* character drive the proton transfer, which leads, in most cases, to a conical intersection of the S1 and S0 surfaces and thus ultrafast internal...

Intersystem crossing processes in nonplanar aromatic heterocyclic molecules.

Abstract: A comprehensive study of the photophysical properties of a series of monoaza[5]helicenes is presented on the basis of joint optical spectroscopy and quantum chemistry investigations. The molecules have been characterized by absorption and CW/time-resolved luminescence measurements. All quantities related to spin-orbit-coupling processes, such as intersystem crossing rates and radiative phosphorescence lifetimes, were found to depend strongly on the nitrogen position within the carbon backbone. Density functional theory and semiempirical quantum-chemical methods were used to evaluate the molecular geometries, the characteristics of the excited singlet and triplet states, and the spin-orbit coupling matrix elements. We demonstrate that the magnitude of spin-orbit coupling is directly correlated with the degree of deviation from planarity. The trends from the calculated photophysical quantities, namely, radiative fluorescence and phosphorescence decay rates and intersystem crossing rates, of the mono-aza-helicenes are fully consistent with experiment.

Structure and Energetics of the Hydronium Hydration Shells

Abstract: Proton solvation and proton mobility are both subjects of great interest in chemistry and biology Here we have studied the hydration shells of H3O+ at temperatures ranging from 260 to 340 K using the multistate empirical valence-bond methodology (MS-EVB2) We have calculated the radial distribution functions for the protonium and its solvation shells Furthermore, we have determined the Gibbs energy and the enthalpy for hydrogen bonds donated or accepted by the first two solvation shells, in comparison to bulk water We find systematic bond-energy differences that appear to agree with a recent IR study on proton hydration Implications of our results to various proton mobility mechanisms are discussed

Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package.

Abstract: Self-consistent charge density functional tight-binding (SCC-DFTB) is a semiempirical method based on density functional theory and has in many cases been shown to provide relative energies and geometries comparable in accuracy to full DFT or ab initio MP2 calculations using large basis sets. This article shows an implementation of the SCC-DFTB method as part of the new QM/MM support in the AMBER 9 molecular dynamics program suite. Details of the implementation and examples of applications are shown.

Ab initio investigation of the complexes between bromobenzene and several electron donors: some insights into the magnitude and nature of halogen bonding interactions.

Abstract: Halogen bonding, a specific intermolecular noncovalent interaction, plays crucial roles in fields as diverse as molecular recognition, crystal engineering, and biological systems. This paper presents an ab initio investigation of a series of dimeric complexes formed between bromobenzene and several electron donors. Such small model systems are selected to mimic halogen bonding interactions found within crystal structures as well as within biological molecules. In all cases, the intermolecular distances are shown to be equal to or below sums of van der Waals radii of the atoms involved. Halogen bonding energies, calculated at the MP2/aug-cc-pVDZ level, span over a wide range, from -1.52 to -15.53 kcal/mol. The interactions become comparable to, or even prevail over, classical hydrogen bonding. For charge-assisted halogen bonds, calculations have shown that the strength decreases in the order OH- > F- > HCO2- > Cl- > Br-, while for neutral systems, their relative strengths attenuate in the order H2CS > H2CO > NH3 > H2S > H2O. These results agree with those of the quantum theory of atoms in molecules (QTAIM) since bond critical points (BCPs) are identified for these halogen bonds. The QTAIM analysis also suggests that strong halogen bonds are more covalent in nature, while weak ones are mostly electrostatic interactions. The electron densities at the BCPs are recommended as a good measure of the halogen bond strength. Finally, natural bond orbital (NBO) analysis has been applied to gain more insights into the origin of halogen bonding interactions.

Ultrafast structural dynamics of water induced by dissipation of vibrational energy.

Abstract: In the liquid phase, water molecules form a disordered fluctuating network of intermolecular hydrogen bonds. Using both inter- and intramolecular vibrations as structural probes in ultrafast infrared spectroscopy, we demonstrate a two-stage structural response of this network to energy disposal: vibrational energy from individually excited water molecules is transferred to intermolecular modes, resulting in a sub-100 fs nuclear rearrangement that leaves the local hydrogen bonds weakened but unbroken. Subsequent energy delocalization over many molecules occurs on an ∼1 ps time scale and is connected with the breaking of hydrogen bonds, resulting in a macroscopically heated liquid.

Detailed chemical kinetic modeling of cyclohexane oxidation.

Abstract: A detailed chemical kinetic mechanism has been developed and used to study the oxidation of cyclohexane at both low and high temperatures. Rules for reaction rate constants are developed for the low-temperature combustion of cyclohexane. These rules can be used for in chemical kinetic mechanisms for other cycloalkanes. Because cyclohexane produces only one type of cyclohexyl radical, much of the low-temperature chemistry of cyclohexane is described in terms of one potential energy diagram showing the reaction of cyclohexyl radical with O2 through five-, six-, and seven-membered-ring transition states. The direct elimination of cyclohexene and HO2 from RO2 is included in the treatment using a modified rate constant of Cavallotti et al. (Proc. Combust. Inst. 2007, 31, 201). Published and unpublished data from the Lille rapid compression machine, as well as jet-stirred reactor data, are used to validate the mechanism. The effect of heat loss is included in the simulations, an improvement on previous studies ...

Stability, reactivity, and aromaticity of compounds of a multivalent superatom.

Abstract: In this article, we analyze the stability, reactivity, and possible aromatic behavior of two recently reported clusters (Reveles, J. U.; Khanna, S. N.; Roach, P. J.; Castleman, A. W., Jr. Proc. Natl. Acad. Sci. 2006, 103, 18405), viz., Al(7)C(-) and Al(7)O(-) in the light of the principles of the maximum hardness and minimum electrophilicity as well as the nucleus-independent chemical shift values. Stability of these clusters in the context of addition/removal of an electron or an Al atom is now clearly understood.

Computational study of thioflavin T torsional relaxation in the excited state.

Abstract: Quantum-chemical calculations of the Thioflavin T (ThT) molecule in the ground S0 and first excited singlet S1 states were carried out. It has been established that ThT in the ground state has a noticeable nonplanar conformation: the torsion angle phi between the benzthiazole and the dimethylaminobenzene rings has been found to be approximately 37 degrees. The energy barriers of the intramolecular rotation appearing at phi = 0 and 90 degrees are quite low: semiempirical AM1 and PM3 methods predict values approximately 700 cm-1 and ab initio methods approximately 1000-2000 cm(-1). The INDO/S calculations of vertical transitions to the S1(abs) excited state have revealed that energy ES1(abs) is minimal for the twisted conformation with phi = 90 degrees and that the intramolecular charge-transfer takes place upon the ThT fragments' rotation from phi = 0 to 90 degrees. Ab initio CIS/RHF calculations were performed to find optimal geometries in the excited S1 state for a series of conformers having fixed phi values. The CIS calculations have predicted a minimum of the S1 state energy at phi approximately 21 degrees; however, the energy values are 1.5 times overestimated in comparison to experimental data. Excited state energy dependence on the torsion angle phi, obtained by the INDO/S method, reveals that ES1(fluor) is minimal at phi = approximately 80-100 degrees, and a plateau is clearly observed for torsion angles ranging from 20 to 50 degrees. On the basis of the calculation results, the following scheme of photophysical processes in the excited S1 state of the ThT is suggested. According to the model, a twisted internal charge-transfer (TICT) process takes place for the ThT molecule in the excited singlet state, resulting in a transition from the fluorescent locally excited (LE) state to the nonfluorescent TICT state, accompanied by torsion angle phi growth from 37 to 90 degrees. The TICT process effectively competes with radiative transition from the LE state and is responsible for significant quenching of the ThT fluorescence in low-viscosity solvents. For viscous solvents or when the ThT molecule is located in a rather rigid microenvironment, for example, when it is bound to amyloid fibrils, internal rotation in the dye molecule is blocked due to steric hindrance, which results in suppression of the LE --> TICT quenching process and in a high quantum yield of fluorescence.