Scaled in Cartesian Coordinates Ab Initio Molecular Force Fields of DNA Bases: Application to Canonical Pairs

The model of Regularized Quantum Mechanical Force Field (RQMFF) was applied to the joint treatment of ab initio and experimental vibrational data of the four primary nucleobases using a new algorithm based on the scaling procedure in Cartesian coordinates. The matrix of scaling factors in Cartesian coordinates for the considered molecules includes diagonal elements for all atoms of the molecule and off-diagonal elements for bonded atoms and for some non-bonded atoms (1–3 and some 1–4 interactions). The choice of the model is based on the results of the second-order perturbation analysis of the Fock matrix for uncoupled interactions using the Natural Bond Orbital (NBO) analysis. The scaling factors obtained within this model as a result of solving the inverse problem (regularized Cartesian scale factors) of adenine, cytosine, guanine, and thymine molecules were used to correct the Hessians of the canonical base pairs: adenine–thymine and cytosine–guanine. The proposed procedure is based on the block structure of the scaling matrix for molecular entities with non-covalent interactions, as in the case of DNA base pairs. It allows avoiding introducing internal coordinates (or coordinates of symmetry, local symmetry, etc.) when scaling the force field of a compound of a complex structure with non-covalent H-bonds

Strategies of Broadband Monitoring Aimed at Minimizing Deposition Errors

This article presents a computational approach for comparing various broadband monitoring strategies, taking into account the positive and negative effects associated with the correlation of thickness errors caused by the monitoring procedure. The approach is based on statistical estimates of the strength of the error self-compensation effect and the expected level of thickness errors. Its application is demonstrated by using a 50-layer, nonpolarizing edge filter. The presented approach is general and can be applied to verify the prospects of broadband monitoring for the production of various types of optical coatings

Online Characterization Algorithms for Optical Coating Production with Broadband Monitoring

Algorithms for the online determination of thicknesses of already-deposited layers are important for the reliable control of optical coating production. Possible ways of constructing such algorithms in the case of coating production with direct broadband monitoring are discussed. A modified triangular algorithm is proposed. In contrast to the well-known triangular algorithm, the new algorithm does not determine all thicknesses of previously deposited layers but only those for which an increase in the accuracy of their determination is to be expected. The most promising algorithms are compared in terms of their accuracy and operational speed. It is shown that the modified triangular algorithm is much faster than the triangular algorithm, and both algorithms have close accuracy. The operational speed of the modified triangular algorithm can be a decisive factor for its use in modern broadband monitoring systems

Electron Diffraction Analysis for the Molecules with Multiple Large-Amplitude Motions. 3‑NitrostyreneA Molecule with Two Internal Rotors

Dynamic structural analysis of the molecules possessing large-amplitude degrees of freedom has been attempted by many researchers; however, so far, electron diffraction investigations involved only one large-amplitude coordinate (internal rotation or bending). The current state of computational facilities allows extending of the general dynamic approach to the systems possessing two or more large-amplitude motions. This paper presents the first practical implementation of the theoretical method developed previously by the authors for solving the dynamic-structural problem with two or more large-amplitude coordinates; the procedure is applied to a molecule of 3-nitrostyrene. The molecule is represented as a set of pseudoconformers built on a two-dimensional grid corresponding to both internal rotation coordinates present in the molecule (with 10–30° steps by each angle); altogether, up to 342 pseudoconformers were used. Structural analysis was based on the experimental electron diffraction data supported by quantum chemical calculations (at the MP2 and B3LYP levels of theory) and molecular spectroscopy data. Quantum chemistry predicts the planar structure of both syn- and anti- stable conformations with close energies and weak interaction between internal rotations of nitro and vinyl groups. The gas-phase electron diffraction experimental data are compatible with the quantum chemical predictions. The principal equilibrium geometry parameters of the molecule (syn- conformation) have been determined as follows: <i>r</i>_e(C–C)_ring, avg. = 1.391(1) Å, <i>r</i>_e(C–C) = 1.477(5) Å, <i>r</i>_e(CC) = 1.333(7) Å, <i>r</i>_e(C–N) = 1.463(5) Å, <i>r</i>_e(NO) = 1.227(3) Å, ∠_e(ONO) = 124.3 (4)°. Experimental data for this molecule are insufficient to make estimates of the barrier heights of internal rotation; the population ratio of syn- and anti- conformations is evaluated as 50 ± 20%. Results of our investigation confirm the presence of significant internal rotations in the 3-nitrostyrene molecule

Study of ultrafast processes in matter by means of time-resolved electron diffraction and microscopy

One of the most fundamental problems of modern natural science is the direct observation of atomic motions in the course of various processes. For this purpose, in the experiment it is necessary to provide high spatial-temporal resolution. The solution to this problem is achieved by using a pulsed electron beam of ultrashort duration to create a stroboscopic diffraction pattern in the method of time-resolved electron diffraction (TRED). Three types of experimental schemes have been developed at our lab. The experimental complex includes (i) 20-keV table-top apparatus for TRED, (ii) 75-keV ultrafast transmission electron microscope and (iii) lensless table-top device for femtosecond electron diffraction. The obtained experimental results are presented

Study of ultrafast processes in matter by means of time-resolved electron diffraction and microscopy

One of the most fundamental problems of modern natural science is the direct observation of atomic motions in the course of various processes. For this purpose, in the experiment it is necessary to provide high spatial-temporal resolution. The solution to this problem is achieved by using a pulsed electron beam of ultrashort duration to create a stroboscopic diffraction pattern in the method of time-resolved electron diffraction (TRED). Three types of experimental schemes have been developed at our lab. The experimental complex includes (i) 20-keV table-top apparatus for TRED, (ii) 75-keV ultrafast transmission electron microscope and (iii) lensless table-top device for femtosecond electron diffraction. The obtained experimental results are presented