Energy Decomposition Scheme for Rectangular Graphene Flakes

We show-to our own surprise-that total electronic energies for a family of m × n rectangular graphene flakes can be very accurately represented by a simple function of the structural parameters m and n with errors not exceeding 1 kcal/mol. The energies of these flakes, usually referred to as multiple zigzag chains Z(m,n), are computed for m, n < 21 at their optimized geometries using the DFTB3 methodology. We have discovered that the structural parameters m and n (and their simple algebraic functions) provide a much better basis for the energy decomposition scheme than the various topological invariants usually used in this context. Most terms appearing in our energy decomposition scheme seem to have simple chemical interpretations. Our observation goes against the well-established knowledge stating that many-body energies are complicated functions of molecular parameters. Our observations might have far-reaching consequences for building accurate machine learning models.

Detection of a C4 Criegee Intermediate: Fourier-Transform Microwave Spectroscopy of Methacrolein Oxide

Pure rotational transitions of methacrolein oxide (MACRO) were observed by Fourier-transform microwave spectroscopy. Among the four low-lying conformers existing within an energy window of 3 kcal/mol, only the lowest-energy conformer, the anti-trans conformer, was detected in a discharged jet of a 1,3-diiode-2-methylprop-1-ene and O2 mixture diluted in Ar. Nineteen pure rotational transitions, in the frequency range from 10 to 25 GHz, most of them showing A/E splitting due to the methyl-top internal rotation, were observed and analyzed by the XIAM program, yielding the internal rotation barrier of 559 cm-1, which very well agrees with a theoretically calculated value, 558 cm-1, at the CCSD(T)/cc-pVTZ level of theory.

Mechanism of proton-coupled electron transfer described with QM/MM implementation of coupled-perturbed density-functional tight-binding

Coupled-perturbed equations for degenerate orbitals were implemented for third order DFTB, which allowed the use of Mulliken charges as reaction coordinates. The method was applied to proton-coupled electron transfer (PCET) reactions in a model system and thoroughly tested for QM and QM/MM setups (i.e., coupled quantum and molecular mechanics). The performed enhanced sampling simulations were stable, and the obtained potentials of the mean force were able to address the thermodynamic and kinetic features of the reactions by showing the expected topography and energy barriers. Hence, this method has the potential to distinguish between concerted and sequential mechanisms, and could next be applied to PCET reactions in more complex systems like proteins.

Spectral Evidence of Bevel-Gear-Type Rotation of Benzene around Br in Solid p-H2: Infrared Spectrum of the C6H6Br Radical

Whether the structure of C₆H₆X (X = halogen), an intermediate in the halogenation of benzene, is an open or a bridged form has been debated. We produced Br to react with C₆H₆ upon photolysis in situ of a Br₂/C₆H₆/p-H₂ matrix at 3.2 K. In contrast to the C₆H₆Cl σ-complex reported previously, the observed infrared spectrum indicates that C₆H₆Br is an open-form π-complex. Furthermore, lines of the two CH out-of-plane bending modes associated mainly with even- and odd-numbered carbons, predicted near 672 and 719 cm^-1, merged into a broad line at 697.3 cm^-1, indicating that these modes become nearly equivalent as Br migrates from one carbon atom to another. Quantum-chemical calculations support that the benzene ring performs a bevel-gear-type rotation with respect to Br. Observation of only trans-ortho- and trans-para-C₆H₆Br₂ suggests that this gear-type motion allows the additional Br atom to attack C₆H₆Br only from the opposite side of the Br atom in C₆H₆Br.

Scanning pH-metry for Observing Reversibility in Protein Folding

One of the main factors affecting protein structure in solution is pH. Traditionally, to study pH-dependent conformational changes in proteins, the concentration of the H+ ions is adjusted manually, complicating real-time analyses, hampering dynamic pH regulation, and consequently leading to a limited number of tested pH levels. Here, we present a programmable device, a scanning pH-meter, that can automatically generate different types of pH ramps and waveforms in a solution. A feedback loop algorithm calculates the required flow rates of the acid/base titrants, allowing one, for example, to generate periodic pH sine waveforms to study the reversibility of protein folding by fluorescence spectroscopy. Interestingly, for some proteins, the fluorescence intensity profiles recorded in such a periodically oscillating pH environment display hysteretic behavior indicating an asymmetry in the sequence of the protein unfolding/refolding events, which can most likely be attributed to their distinct kinetics. Another useful application of the scanning pH-meter concerns coupling it with an electrospray ionization mass spectrometer to observe pH-induced structural changes in proteins as revealed by their varying charge-state distributions. We anticipate a broad range of applications of the scanning pH-meter developed here, including protein folding studies, determination of the optimum pH for achieving maximum fluorescence intensity, and characterization of fluorescent dyes and other synthetic materials.

Structures of Pyridine-Water Clusters Studied with Infrared-Vacuum Ultraviolet Spectroscopy

The infrared (IR) spectra of the O-H stretching vibrations of pyridine-water clusters (Pyd)_m(H₂O)_n, with m, n = 1-4, have been investigated with infrared-vacuum ultraviolet (VUV) spectroscopy under a jet-cooled condition. The time-of-flight mass spectrum of (Pyd)_m(H₂O)_n⁺ by VUV ionization at ∼9 eV showed an unusual intensity pattern with very weak ion signals for m = 1 and 2 and stronger signals for m ≥ 3. This unusual mass pattern was explained by a drastic structural change of (Pyd)_m(H₂O)_n upon the VUV ionization, which was followed by the elimination of water molecules. Among the recorded IR spectra, only one spectrum monitored, (Pyd)₂⁺ cation, showed a well-resolved structure. The spectrum was analyzed by comparing with the simulated ones of possible stable isomers of (Pyd)₂(H₂O)_n, which were obtained with quantum-chemical calculations. Most of the calculated (Pyd)₂(H₂O)_n clusters had the characteristic structure in which H₂O or (H₂O)₂ forms a hydrogen-bonded bridge between two pyridines to form the π-stacked (Pyd)₂, and an additional H₂O molecule(s) extends the H-bonded network. The π-stacked (Pyd)₂(H₂O)_n moiety is very stable and is thought to exist as a local structure in a pyridine/water mixed solution. The Fermi resonance between the O-H stretch fundamentals and the overtones of the O-H bending vibrations in (Pyd)_m(H₂O)_n was found to be less pronounced in the case of (Pyd)_m(NH₃)_n studied previously.

Vacuum Ultraviolet Photoionization Induced Proton Migration and Formation of a New C-N Bond in Pyridine Clusters Revealed by Infrared Spectroscopy and Mass Spectrometry

The structures and reactions of pyridine (Pyd) cluster cations in a supersonic molecular beam generated upon photoionization at 9.2-9.4 eV were investigated by infrared (IR) action spectroscopy. The mass spectrum showed prominent peaks of (Pyd)_m⁺ and H⁺(Pyd)_m, m = 1-5. In the pyridine/pyridine-d₅ mixture, the mass pattern indicated that H⁺ and D⁺ migrated during the formation and dissociation of the cluster cations. The IR photodissociation spectra of both (Pyd)₂⁺ and H⁺(Pyd)₂ revealed a N-H stretching band near 3400 cm^-1, indicating that their structures are 1-(2-pyridyl)pyridin-1-ium and pyridinium-pyridine, respectively. Observation of the former product implies that the reaction proceeds via an α-distonic cation intermediate, while the latter product is formed via proton migration. The IR spectra of (Pyd)_m⁺ and H⁺(Pyd)_m, m ≥ 3, suggested that these clusters consist of a covalently bound (Pyd)₂⁺ or H⁺(Pyd)₂ core, respectively, with additional pyridines attached to them via hydrogen bonds and/or weak dispersive interactions.

Zhang-Zhang Polynomials of Multiple Zigzag Chains Revisited: A Connection with the John-Sachs Theorem

Multiple zigzag chains Zm,n of length n and width m constitute an important class of regular graphene flakes of rectangular shape. The physical and chemical properties of these basic pericondensed benzenoids can be related to their various topological invariants, conveniently encoded as the coefficients of a combinatorial polynomial, usually referred to as the ZZ polynomial of multiple zigzag chains Zm,n. The current study reports a novel method for determination of these ZZ polynomials based on a hypothesized extension to John–Sachs theorem, used previously to enumerate Kekulé structures of various benzenoid hydrocarbons. We show that the ZZ polynomial of the Zm,n multiple zigzag chain can be conveniently expressed as a determinant of a Toeplitz (or almost Toeplitz) matrix of size m2×m2 consisting of simple hypergeometric polynomials. The presented analysis can be extended to generalized multiple zigzag chains Zkm,n, i.e., derivatives of Zm,n with a single attached polyacene chain of length k. All presented formulas are accompanied by formal proofs. The developed theoretical machinery is applied for predicting aromaticity distribution patterns in large and infinite multiple zigzag chains Zm,n and for computing the distribution of spin densities in biradical states of finite multiple zigzag chains Zm,n.

Density-Functional Tight-Binding Parameters for Bulk Zirconium: A Case Study for Repulsive Potentials

Density-functional tight-binding (DFTB) parameters are presented for the simulation of the bulk phases of zirconium. Electronic parameters were obtained using a band structure fitting strategy, while two-center repulsive potentials were created by particle swarm optimization. As objective functions for the repulsive potential fitting, we employed the Birch-Murnaghan equations of state for hexagonal close-packed (HCP), body-centered cubic (BCC) and ω phases of Zr from density-functional theory (DFT). When fractional atomic coordinates are not allowed to change in the generation of the equation-of-state curves, long-range repulsive DFTB potentials are able to almost perfectly reproduce equilibrium structures, relative DFT energies of the bulk phases, and bulk moduli. However, the same potentials lead to artifacts in the DFTB potential energy surfaces when atom positions in the unit cell are allowed to fully relax during the change of unit cell parameters. Conventional short-range repulsive DFTB potentials, while inferior in their ability to reproduce DFT bulk energetics, are able to correctly reproduce the qualitative shape of the DFT potential energy surfaces, including the location of global minima, and can therefore be considered more transferable.

Sample Flow Rate Scan in Electrospray Ionization Mass Spectrometry Reveals Alterations in Protein Charge State Distribution

Sample flow rate is one of the parameters that influence the sensitivity of electrospray ionization (ESI) mass spectrometry. By varying the sample flow rate, initial droplets of different sizes can be generated. Protein molecules in small droplets may form gas-phase ions earlier than the ones in large droplets. Here, we have systematically studied the influence of sample flow rate on the ESI charge state distributions (CSDs) of model proteins. A dedicated programmable sample flow rate scanner was used to infuse protein samples at different flow rates into a mass spectrometer. The synergistic influence of sample flow rate and various electrolytes (ammonium acetate, ammonium bicarbonate, ammonium formate, and piperidine) was studied. Significant alterations to the CSDs with increasing flow rate were observed. For example, in the presence of ammonium acetate, at low flow rates, lower charge states of proteins showed high intensities, while at high flow rates, ions related to higher charge states of proteins dominated the spectra. On the other hand, in the presence of piperidine, a significant reduction in the ion currents of all charge states was observed during the flow rate scan. Our observations suggest that at low flow rates the protein molecules follow a charged residue model of ionization mechanism, and at high flow rates-due to structural changes in protein molecules in large ESI droplets-the charged residue and chain ejection models can possibly coexist. We propose the use of sample flow rate scan as a way to reveal the influence of flow rate on the CSDs of the studied proteins.

Telechemistry: monitoring chemical reactionsviathe cloud using the Particle Photon Wi-Fi module

A popular electronic module and the associated Internet-of-Things tools provide chemists with more control over long-term experimental procedures and enhance lab work safety.

Chemical clocks, oscillations, and other temporal effects in analytical chemistry: oddity or viable approach?

Most analytical methods are based on "analogue" inputs from sensors of light, electric potentials, or currents. The signals obtained by such sensors are processed using certain calibration functions to determine concentrations of the target analytes. The signal readouts are normally done after an optimised and fixed time period, during which an assay mixture is incubated. This minireview covers another-and somewhat unusual-analytical strategy, which relies on the measurement of time interval between the occurrences of two distinguishable states in the assay reaction. These states manifest themselves via abrupt changes in the properties of the assay mixture (e.g. change of colour, appearance or disappearance of luminescence, change in pH, variations in optical activity or mechanical properties). In some cases, a correlation between the time of appearance/disappearance of a given property and the analyte concentration can be also observed. An example of an assay based on time measurement is an oscillating reaction, in which the period of oscillations is linked to the concentration of the target analyte. A number of chemo-chronometric assays, relying on the existing (bio)transformations or artificially designed reactions, were disclosed in the past few years. They are very attractive from the fundamental point of view but-so far-only few of them have be validated and used to address real-world problems. Then, can chemo-chronometric assays become a practical tool for chemical analysis? Is there a need for further development of such assays? We are aiming to answer these questions.

Polarizability tensor invariants of H2, HD, and D2

We report an exhaustive compilation of wavelength-dependent matrix elements over the mean polarizability (α¯) and polarizability anisotropy (γ) operators for the rovibrational states of the H₂, HD, and D₂ molecules together with an accompanying computer program for their evaluation. The matrix elements can be readily evaluated using the provided codes for rovibrational states with J = 0-15 and v = 0-4 and for any laser wavelengths in the interval 182.25-1320.6 nm corresponding to popular, commercially available lasers. The presented results substantially extend the scope of the data available in the literature, both in respect of the rovibrational transitions analyzed and the range of covered laser frequencies. The presented detailed tabulation of accurate polarizability tensor invariants is essential for successful realization of our main long-term goal: developing a universal standard for determining absolute Raman cross sections and absolute Raman intensities in experimental Rayleigh and Raman scattering studies of molecules.

Nucleotide-Dependent Bioautocatalytic Timer Reaction

We describe a biochemical timer composed of three biocatalytic reactions involving three types of adenylate nucleotides: adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP). The timer is triggered by a small amount of ATP or ADP. An abrupt increase in the ATP concentration (following numerous amplification cycles) leads to a sudden increase of luminescence from the reaction mixture. The time point when the luminescence appears is found to be a function of the initial concentration of the triggering nucleotide (5.0 × 10(-8)-1.0 × 10(-6) M), even in the presence of a complex biological matrix. The mechanism of the observed dependence of the time of luminescence increase on the concentration has been confirmed with simple kinetic models. Due to the biocompatibility of the proposed trienzymatic reaction scheme (sensitivity to common nucleotides and occurrence in a neutral pH aqueous environment), the scheme can be used in bioengineered systems that require modulation of the response time (light emission) by concentration.

Infrared identification of the Criegee intermediates syn- and anti-CH₃CHOO, and their distinct conformation-dependent reactivity

The Criegee intermediates are carbonyl oxides that play critical roles in ozonolysis of alkenes in the atmosphere. So far, the mid-infrared spectrum of only the simplest Criegee intermediate CH2OO has been reported. Methyl substitution of CH2OO produces two conformers of CH3CHOO and consequently complicates the infrared spectrum. Here we report the transient infrared spectrum of syn- and anti-CH3CHOO, produced from CH3CHI + O2 in a flow reactor, using a step-scan Fourier-transform spectrometer. Guided and supported by high-level full-dimensional quantum calculations, rotational contours of the four observed bands are simulated successfully and provide definitive identification of both conformers. Furthermore, anti-CH3CHOO shows a reactivity greater than syn-CH3CHOO towards NO/NO2; at the later period of reaction, the spectrum can be simulated with only syn-CH3CHOO. Without NO/NO2, anti-CH3CHOO also decays much faster than syn-CH3CHOO. The direct infrared detection of syn- and anti-CH3CHOO should prove useful for field measurements and laboratory investigations of the Criegee mechanism.

Quantum chemical investigation of epoxide and ether groups in graphene oxide and their vibrational spectra

We present a detailed analysis of the factors influencing the formation of epoxide and ether groups in graphene nanoflakes using conventional density functional theory (DFT), the density-functional tight-binding (DFTB) method, π-Hückel theory, and graph theoretical invariants. The relative thermodynamic stability associated with the chemisorption of oxygen atoms at various positions on hexagonal graphene flakes (HGFs) of D(6h)-symmetry is determined by two factors - viz. the disruption of the π-conjugation of the HGF and the geometrical deformation of the HGF structure. The thermodynamically most stable structure is achieved when the former factor is minimized, and the latter factor is simultaneously maximized. Infrared (IR) spectra computed using DFT and DFTB reveal a close correlation between the relative thermodynamic stabilities of the oxidized HGF structures and their IR spectral activities. The most stable oxidized structures exhibit significant IR activity between 600 and 1800 cm(-1), whereas less stable oxidized structures exhibit little to no activity in this region. In contrast, Raman spectra are found to be less informative in this respect.

Relative isomer abundance of fullerenes and carbon nanotubes correlates with kinetic stability

A methodology to evaluate the kinetic stability of carbon nanostructures is presented based on the assumption of the independent and random nature of thermal vibrations. The kinetic stability is directly correlated to the cleavage probability for the weakest bond of a given nanostructure. The application of the presented method to fullerenes and carbon nanotubes yields clear correlation to their experimentally observed relative isomer abundances. The general and simple formulation of the method ensures its applicability to other nanostructures for which formation is controlled by kinetic factors.

Theoretical interpretation of the UV-vis spectrum of the CS2/Cl complex in the spectral region 320-550 nm

Accurate multireference configuration interaction and time-dependent density functional calculations have been performed to interpret the experimental UV-vis spectrum of the CS(2)/Cl complex in the spectral region 320-550 nm. The molecular structure of the complex responsible for the previously observed UV-vis spectrum is recognized as ClSCS, not ClCS(2). Two low-lying excited states of ClSCS, responsible for its optical absorption, have been identified and analyzed. Optical excitation of ClSCS leads to the excitation-specific bond elongation that may lead to photofragmentation of the molecule. In addition, experimental conditions for verifying the presence of ClCS(2) are identified and detailed characterization of its optically active excited states with possible photofragmentation pathways is given.

Convergence in the evolution of nanodiamond Raman spectra with particle size: a theoretical investigation

Structural characterization of nanodiamonds by vibrational spectroscopy requires knowledge of the factors determining the spectra. Raman spectroscopy is widely used to detect the diamond phase in nanodiamond powders and films, but several spectral features are still poorly understood. Here we present a theoretical study of the evolution of diamond hydrocarbon Raman spectra with increasing size, from the adamantane molecule to approximately 3 nm large tetrahedral and octahedral particles of T(d) symmetry, containing up to about 1000 carbon atoms. The self-consistent-charge density functional tight-binding method (SCC-DFTB) was used for the calculation of harmonic first-order Raman spectra. We demonstrate very good agreement with Raman spectra computed by standard density functional theory (DFT) for the smaller model systems. The evolution of the Raman patterns is smooth, and convergence to the bulk limit could clearly be observed in case of the acoustic vibrational modes (omega(A) = 0 cm(-1)). We found a simple relationship between nanodiamond size and vibrational frequency, which is analogous to the corresponding equation for the radial breathing mode of single-walled carbon nanotubes. The T(2) modes of octahedral diamond hydrocarbons coalesce faster to the bulk optical vibrational mode (in experiment, omega(O) = 1332 cm(-1)) than those of tetrahedral particles, consistent with the fact that the bulk/surface ratio is more favorable for octahedral particles. Our simulations unequivocally show that controversial Raman features around 500 and 1150 cm(-1) do not originate from the nanodiamond crystals, and that the nanocrystal shape plays an important role in the appearance of the Raman spectra even in the 3 nm domain.

Multireference perturbation theory can predict a false ground state

Prediction of a false ground state with popular variants of multireference perturbation theory (CASPT2 and MRMP) is reported for a remarkably simple chemical system: the Sc(2) molecule.