Computational analyses of the vibrational spectra of fentanyl, carfentanil and remifentanil.

The infrared (IR) spectra of fentanyl, carfentanil and remifentanil, and protonated salts, are computed using quantum chemistry methods. New experimental FTIR spectra are also reported and compared to the calculations. The accuracy of two density functional theory methods, B3LYP and M06-2X, are tested against higher level theories (MP2) and the experimental data. Gas phase IR spectra are calculated for both the neutral and protonated molecules in order to compare with the experimental data measured for various salts of fentanyl and its analogues. Key vibrational modes are selected and studied in detail using a vibrational mode locality calculation. The main contributing atomic movements in these vibrational modes are identified.

Analytic Route to Tunneling Splittings Using Semiclassical Perturbation Theory.

We present an efficient, analytical, and simple route to approximating tunneling splittings in multidimensional chemical systems, directly from ab initio computations. The method is based on the Wentzel-Kramers-Brillouin (WKB) approximation combined with the vibrational perturbation theory. Anharmonicity and corner-cutting effects are implicitly accounted for without requiring a full potential energy surface. We test this method on the following three systems: a model one-dimensional double-well potential, the isomerization of malonaldehyde, and the isomerization of tropolone. The method is shown to be efficient and reliable.

Soft windowing application to improve analysis of high-throughput phenotyping data.

MOTIVATION: High-throughput phenomic projects generate complex data from small treatment and large control groups that increase the power of the analyses but introduce variation over time. A method is needed to utlize a set of temporally local controls that maximizes analytic power while minimizing noise from unspecified environmental factors. RESULTS: Here we introduce 'soft windowing', a methodological approach that selects a window of time that includes the most appropriate controls for analysis. Using phenotype data from the International Mouse Phenotyping Consortium (IMPC), adaptive windows were applied such that control data collected proximally to mutants were assigned the maximal weight, while data collected earlier or later had less weight. We applied this method to IMPC data and compared the results with those obtained from a standard non-windowed approach. Validation was performed using a resampling approach in which we demonstrate a 10% reduction of false positives from 2.5 million analyses. We applied the method to our production analysis pipeline that establishes genotype-phenotype associations by comparing mutant versus control data. We report an increase of 30% in significant P-values, as well as linkage to 106 versus 99 disease models via phenotype overlap with the soft-windowed and non-windowed approaches, respectively, from a set of 2082 mutant mouse lines. Our method is generalizable and can benefit large-scale human phenomic projects such as the UK Biobank and the All of Us resources. AVAILABILITY AND IMPLEMENTATION: The method is freely available in the R package SmoothWin, available on CRAN http://CRAN.R-project.org/package=SmoothWin. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Calculations on the unimolecular decomposition of the nerve agent VX.

It is very difficult to perform experiments on the physical parameters for the thermal decomposition of chemical nerve agents such as VX and computations, therefore, are useful. The reaction dynamics of the gas-phase pericyclic hydrogen transfer of the nerve agent VX is studied computationally. The geometries of the stationary structures are calculated at M06-2X/jul-cc-pVTZ level of theory. Single point energy calculations are carried out at the CBS/QB3 level to correct the energy barriers. Canonical reaction rate constants are calculated as a function of temperature. The one-dimensional semiclassical transition state theory is used to analyse the quantum tunneling effects. A reduced-dimensional hindered rotor model is proposed, tested, and applied to calculate the vibrational partition functions. It is found that the ester (O-side) and thioester (S-side) side chains of VX undergo pericyclic H-transfer reactions that result in decomposition of the molecule. The S-side reaction is favoured both kinetically and thermodynamically and dominates the pyrolysis over the temperature range from 600 K to 1000 K. It is predicted that VX completely decomposes in 2 s at temperatures above 750 K.

Hydrogen tunnelling in the rearrangements of carbenes: the role of dynamical calculations.

Tunnelling controlled chemical reactions are those which preferably proceed through pathways with high but narrow potential energy barriers, via quantum tunnelling, resulting in a product that would be disfavoured classically. These reactions are very sensitive to barrier width, height and temperature and so dynamical theoretical methods are required to describe these processes. Recent experimental work on charge-tagged phenyl pyruvic acid derivatives has found, in contrast to similar systems, no evidence of tunnelling control. Using semiclassical transition state theory, we rationalise these results and find tunnelling is significant in this system.

New Developments in Semiclassical Transition-State Theory.

This Feature Article describes some recent developments and applications of the Semiclassical Transition-State Theory (SCTST) for treating quantum tunneling in chemical reactions. A reduced dimensional form of the SCTST is discussed and is shown to be particularly efficient, as the required number of electronic structure calculations is reduced to an absolute minimum. We also describe how an alternative formulation of SCTST developed by Hernandez and Miller [ Chem. Phys. Lett. 1993 , 214 , 129 ], the SCTST-θ, has advantages in allowing for straightforward applications of the SCTST for any form of the potential expansion at the transition state. We also illustrate the power of SCTST in applications to more complex systems. We show how polyatomic modes such as internal rotations and torsions can be treated efficiently in SCTST calculations. We also describe some applications of the method to hydrogen atom tunneling in unimolecular reactions including the degradation of chemical nerve agents and the decay of the atmospherically important Criegee intermediates.

Erratum: Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts.

[This corrects the article DOI: 10.1038/s42003-018-0226-0.].

Theoretical Study of Gas-Phase Unimolecular Decomposition of Simulants of the Nerve Agent VX.

In order to further understand and support approaches for the degradation and destruction of toxic chemicals, the thermal decomposition of the nerve agent VX through possible pericyclic hydrogen transfer reactions is investigated using simulant molecules. A total of four simulant molecules are studied. Three of them have only one possible H-transfer site, while the other has two. They are chosen to bring physical insights into individual steps of the pericyclic reaction mechanism as well as the possible existence of competing mechanisms. The unimolecular reaction rate constants at the high-pressure limit are calculated. Geometries of stationary structures on the potential energy surfaces are calculated with the MP2 method as well as the B3LYP and M06-2X functionals and 6-311++G(d,p), jul-cc-pVTZ, and aug-cc-pVTZ basis sets. The barrier heights are corrected using energy values obtained at the CBS/QB3 level of theory. The contribution of the quantum tunneling effect to the reaction rate constants is included using one-dimensional semiclassical transition state theory. Adiabatic barrier heights, reaction rate constants, and branching ratio of the competing mechanisms are reported.

Identification of genes required for eye development by high-throughput screening of mouse knockouts.

Despite advances in next generation sequencing technologies, determining the genetic basis of ocular disease remains a major challenge due to the limited access and prohibitive cost of human forward genetics. Thus, less than 4,000 genes currently have available phenotype information for any organ system. Here we report the ophthalmic findings from the International Mouse Phenotyping Consortium, a large-scale functional genetic screen with the goal of generating and phenotyping a null mutant for every mouse gene. Of 4364 genes evaluated, 347 were identified to influence ocular phenotypes, 75% of which are entirely novel in ocular pathology. This discovery greatly increases the current number of genes known to contribute to ophthalmic disease, and it is likely that many of the genes will subsequently prove to be important in human ocular development and disease.

Spiers Memorial Lecture. Introductory lecture: quantum dynamics of chemical reactions.

This Spiers Memorial Lecture discusses quantum effects that can be calculated and observed in the chemical reactions of small molecules. This includes quantum reactive scattering resonances, vibrational and rotational state effects, and quantum tunnelling in chemical reactions. Both experimental and theoretical advances are reviewed. Of particular emphasis is a description of the development of reduced dimensional theories which can highlight chemical reactions that are likely to be of interest for more accurate quantum reactive scattering studies and new experiments. Furthermore, the reduced dimensional models allow for the development and testing of computationally inexpensive procedures that enable calculations to be performed on quantum effects in reactions of larger polyatomic molecules.

Catalysis and tunnelling in the unimolecular decay of Criegee intermediates.

The unimolecular decay of Criegee intermediates is the major producer of OH radicals in the atmosphere. Here, Semi-Classical Transition State Theory (SCTST) in full and reduced dimensions is used to determine thermal rate constants for their unimolecular decay, as well as their decay catalysed by a single water molecule. These reactions shed light on the applicability of SCTST for catalysed hydrogen transfer reactions.

Application of one-dimensional semiclassical transition state theory to the CH3OH + H ⇌ CH2OH/CH3O + H2 reactions.

The rate constants of the two branches of H-abstractions from CH3OH by the H-atom and the corresponding reactions in the reverse direction are calculated using the one-dimensional semiclassical transition state theory (1D SCTST). In this method, only the reaction mode vibration of the transition state (TS) is treated anharmonically, while the remaining internal degrees of freedom are treated as they would have been in a standard TS theory calculation. A total of eight ab initio single-point energy calculations are performed in addition to the computational cost of a standard TS theory calculation. This allows a second-order Richardson extrapolation method to be employed to improve the numerical estimation of the third- and fourth-order derivatives, which in turn are used in the calculation of the anharmonic constant. Hindered-rotor (HR) vibrations are identified in the equilibrium states of CH3OH and CH2OH, and the TSs of the reactions. The partition function of the HRs are calculated using both a simple harmonic oscillator model and a more sophisticated one-dimensional torsional eigenvalue summation (1D TES) method. The 1D TES method can be easily adapted in 1D SCTST computation. The resulting 1D SCTST with 1D TES rate constants show good agreement to previous theoretical and experimental works. The effects of the HR on rate constants for different reactions are also investigated.This article is part of the theme issue 'Modern theoretical chemistry'.

Recent advances in quantum scattering calculations on polyatomic bimolecular reactions.

This review surveys quantum scattering calculations on chemical reactions of polyatomic molecules in the gas phase published in the last ten years. These calculations are useful because they provide highly accurate information on the dynamics of chemical reactions which can be compared in detail with experimental results. They also serve as quantum mechanical benchmarks for testing approximate theories which can more readily be applied to more complicated reactions. This review includes theories for calculating quantities such as rate constants which have many important scientific applications.

A Combined Theoretical and Experimental Study of Sarin (GB) Decomposition at High Temperatures.

Theoretical and experimental results are presented for the pyrolytic decomposition of the nerve agent sarin (GB) in the gas phase. High-level quantum chemistry calculations are performed together with a semiclassical transition-state theory for describing quantum mechanical tunneling. The experimental and theoretical results for the temperature dependence of the survival times show very good agreement, as does the calculated and measured activation energy for thermal decomposition. The combined results suggest that the thermal decomposition of GB, for temperature ranging from 350 to 500 °C, goes through a pericyclic reaction mechanism with a transition state consisting of a six-membered ring structure.