Terahertz spectroscopy of 2,4,6-trinitrotoluene molecular solids from first principles

• Ido Azuri,
• Anna Hirsch,
• Anthony M. Reilly,
• Alexandre Tkatchenko,
• Shai Kendler,
• Oded Hod and
• Leeor Kronik

Beilstein J. Org. Chem. 2018, 14, 381–388, doi:10.3762/bjoc.14.26

• Science, Tel Aviv University, Tel Aviv 6997801, Israel 10.3762/bjoc.14.26 Abstract We present a computational analysis of the terahertz spectra of the monoclinic and the orthorhombic polymorphs of 2,4,6-trinitrotoluene. Very good agreement with experimental data is found when using density functional

• . Keywords: density functional theory; THz spectroscopy; Introduction The transparency of many non-conductive materials in the terahertz range (0.1 to 10 THz) of the electromagnetic spectrum has led to the development of several potential applications of terahertz radiation [1]. Terahertz spectroscopy of

• yield reliable simulated spectra for complex materials is density functional theory (DFT) [23]. A significant complication, however, is that conventionally used exchange–correlation energy functionals in DFT do not describe the intermolecular dispersion interactions well. Therefore, early calculations

Recent advances on organic blue thermally activated delayed fluorescence (TADF) emitters for organic light-emitting diodes (OLEDs)

• Thanh-Tuân Bui,
• Fabrice Goubard,
• Malika Ibrahim-Ouali,
• Didier Gigmes and
• Frédéric Dumur

Beilstein J. Org. Chem. 2018, 14, 282–308, doi:10.3762/bjoc.14.18

• maintaining a large optical bandgap. In fact, dihedral angles of 49.9, 86.8, 71.4 and 82.4° were determined by density functional theory (DFT) calculations between the donor plane and the acceptor plane for T20–T23, respectively. Due to its lesser twisted structure and based on the design rule previously

Stereochemical outcomes of C–F activation reactions of benzyl fluoride

• Neil S. Keddie,
• Pier Alexandre Champagne,
• Justine Desroches,
• Jean-François Paquin and
• David O'Hagan

Beilstein J. Org. Chem. 2018, 14, 106–113, doi:10.3762/bjoc.14.6

• fluoride substrates (Figure 1), producing the corresponding substituted products in moderate to good yields. The water/isopropanol system was also shown to be amenable to phenolate and thiolate nucleophiles [3]. Previously, Paquin et al. undertook density functional theory (DFT) studies on the mechanism of

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• richer in bands than a typical ECD spectrum (just like IR spectra vs UV–vis spectra) [1][4][36]. Nowadays, density functional theory (DFT) allows a calculation of the VCD spectrum of a chiral molecule, which then can be compared with the measured VCD spectrum and by this the absolute configuration (AC

Halogen-containing thiazole orange analogues – new fluorogenic DNA stains

• Aleksey A. Vasilev,
• Meglena I. Kandinska,
• Stanimir S. Stoyanov,
• Stanislava B. Yordanova,
• David Sucunza,
• Juan J. Vaquero,
• Obis D. Castaño,
• Stanislav Baluschev and
• Silvia E. Angelova

Beilstein J. Org. Chem. 2017, 13, 2902–2914, doi:10.3762/bjoc.13.283

• position) are presented in Figure 5 with the respective atom color scheme. The electronic reorganizations upon excitation were probed using time-dependent density functional theory (TDDFT) calculations. TDPBE0 (time-dependent density functional theory calculations using Perdew–Burke–Ernzerhof exchange

¹⁵N-Labelling and structure determination of adamantylated azolo-azines in solution

• Sergey L. Deev,
• Alexander S. Paramonov,
• Tatyana S. Shestakova,
• Igor A. Khalymbadzha,
• Oleg N. Chupakhin,
• Julia O. Subbotina,
• Oleg S. Eltsov,
• Pavel A. Slepukhin,
• Vladimir L. Rusinov,
• Alexander S. Arseniev and
• Zakhar O. Shenkarev

Beilstein J. Org. Chem. 2017, 13, 2535–2548, doi:10.3762/bjoc.13.250

• analysis in the 1D 13С spectra acquired with selective 15N decoupling, respectively. Additional spin–spin interactions were detected in the 15N-HMBC spectra. NMR data and DFT (density functional theory) calculations permitted to suggest a possible mechanism of isomerization for the adamantylated products

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• -energy nπ* states are not present. This explanation is further substantiated using time-dependent density functional (TD-DFT) computations for pyrene–adenine conjugates 3 and 5. The molecular structures of compounds 3 and 5 were optimized at the B3LYP/6-311G(d,p) theory level. For the ground state

• using the density functional theory (DFT) with the hybrid gradient corrected correlation functional B3LYP [38] and Gaussian-type basis functions 6-311G(d,p) [39]. TD-DFT calculations were performed in the optimized ground state geometry using the same B3LYP functional and basis sets. Five lowest singlet

Syntheses, structures, and stabilities of aliphatic and aromatic fluorous iodine(I) and iodine(III) compounds: the role of iodine Lewis basicity

• Tathagata Mukherjee,
• Soumik Biswas,
• Andreas Ehnbom,
• Subrata K. Ghosh,
• Ibrahim El-Zoghbi,
• Nattamai Bhuvanesh,
• Hassan S. Bazzi and
• John A. Gladysz

Beilstein J. Org. Chem. 2017, 13, 2486–2501, doi:10.3762/bjoc.13.246

• ][67][68]. Calculations. Computations were performed with the Gaussian09 program package, employing the ultrafine grid (99,590) to enhance accuracy [69]. Geometries were optimized using density functional theory (DFT). The B3LYP [70][71][72] functional was employed with an all-electron 6-311+G(d,p) [73

Synthesis, effect of substituents on the regiochemistry and equilibrium studies of tetrazolo[1,5-a]pyrimidine/2-azidopyrimidines

• Elisandra Scapin,
• Paulo R. S. Salbego,
• Caroline R. Bender,
• Alexandre R. Meyer,
• Anderson B. Pagliari,
• Tainára Orlando,
• Geórgia C. Zimmer,
• Clarissa P. Frizzo,
• Helio G. Bonacorso,
• Nilo Zanatta and
• Marcos A. P. Martins

Beilstein J. Org. Chem. 2017, 13, 2396–2407, doi:10.3762/bjoc.13.237

• (R in the 4-position of the ring), which was attributed to an equilibrium of azide–tetrazole. In the solid state, all compounds were found as 2-azidopyrimidines. The regiochemistry of the reaction and the stability of the products are discussed on the basis of the data obtained by density functional

• , using ionic liquids and water as solvents, and short reaction times. In addition, 5-substituted isomers have proved to be excellent models in carrying out a thorough investigation of the azide–tetrazole equilibrium mechanism by density functional theory (DFT) and various experimental methods (e.g., NMR

Synthesis and photophysical properties of novel benzophospholo[3,2-b]indole derivatives

• Mio Matsumura,
• Mizuki Yamada,
• Atsuya Muranaka,
• Misae Kanai,
• Naoki Kakusawa,
• Daisuke Hashizume,
• Masanobu Uchiyama and
• Shuji Yasuike

Beilstein J. Org. Chem. 2017, 13, 2304–2309, doi:10.3762/bjoc.13.226

• corresponding vibronic band was seen in the absorption spectrum at 330–340 nm. Density functional theory (DFT) calculations [38] were carried out at the B3LYP/LanL2DZ level of theory. The HOMO and LUMO energies of the selected compounds are given in Table 3. For fluorescent compounds 3, 4, 7, and 9, the HOMO

Are boat transition states likely to occur in Cope rearrangements? A DFT study of the biogenesis of germacranes

• José Enrique Barquera-Lozada and
• Gabriel Cuevas

Beilstein J. Org. Chem. 2017, 13, 1969–1976, doi:10.3762/bjoc.13.192

• elemanschkuhriolide, but this transition state is questionable due to its high energy. The possible mechanisms of this transformation were studied in the density functional theory frame. The mechanistic differences between the transformation of (Z,E)-germacranes and (E,E)-germacranes were also studied. We found that

• stable elemanolide that is even more stable than its (Z,E)-germacrane. Keywords: biogenesis; density functional theory; reaction mechanism; sigmatropic rearrangement; terpenes; Introduction Germacranes are biogenetic precursors of elemanes [1][2][3][4], because germacranes can be easily transformed

• , stabilizing the transition state, or destabilizing the ground states energy of the reactants. An antibody-catalyzed oxy-Cope reaction has already been described [42] as well as a proposed reaction mechanism [43]. In the study presented in this paper, we performed density functional theory (DFT) calculations

Theoretical simulation of the infrared signature of mechanically stressed polymer solids

• Matthew S. Sammon,
• Milan Ončák and
• Martin K. Beyer

Beilstein J. Org. Chem. 2017, 13, 1710–1716, doi:10.3762/bjoc.13.165

• and widening of bond angles, which changes the infrared spectrum. Here, the infrared spectrum of solid polymer samples exposed to mechanical stress is simulated by density functional theory calculations. Mechanical stress is described with the external force explicitly included (EFEI) method. The

• infrared bands is not a shift of the peak position, but rather peak broadening and a characteristic change in the relative intensities of the strongest bands, which may serve for the identification and quantification of mechanical stress in polymer solids. Keywords: density functional theory; infrared

Correction: Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis

• Stephanie R. Hare and
• Dean J. Tantillo

Beilstein J. Org. Chem. 2017, 13, 1669–1669, doi:10.3762/bjoc.13.161

• Stephanie R. Hare Dean J. Tantillo Department of Chemistry, University of California–Davis, 1 Shields Avenue, Davis, CA 95616, USA 10.3762/bjoc.13.161 Keywords: carbocation; density functional theory; dynamics; mechanism; terpene; The originally published Figure 6 had several mis-drawn

Strategies toward protecting group-free glycosylation through selective activation of the anomeric center

• A. Michael Downey and
• Michal Hocek

Beilstein J. Org. Chem. 2017, 13, 1239–1279, doi:10.3762/bjoc.13.123

Sugar-based micro/mesoporous hypercross-linked polymers with in situ embedded silver nanoparticles for catalytic reduction

• Qing Yin,
• Qi Chen,
• Li-Can Lu and
• Bao-Hang Han

Beilstein J. Org. Chem. 2017, 13, 1212–1221, doi:10.3762/bjoc.13.120

• (BET) of SugPOP-1 was found to be as high as 1220 m2 g−1 and about 1000 m2 g−1 for SugPOP-2 and SugPOP-3. The PSD profiles for all polymers (based on the nonlinear density functional theory (NLDFT) method) are shown in Figure 2b. The dominant PSD peaks for polymer SugPOP-2 are located at around 0.53

Correlation of surface pressure and hue of planarizable push–pull chromophores at the air/water interface

• Frederik Neuhaus,
• Fabio Zobi,
• Gerald Brezesinski,
• Marta Dal Molin,
• Stefan Matile and
• Andreas Zumbuehl

Beilstein J. Org. Chem. 2017, 13, 1099–1105, doi:10.3762/bjoc.13.109

• the density functional level of theory (DFT) in order to estimate an average value of the height and area of the same (details are given in the Experimental section and in Supporting Information File 1). The calculations indicate that, in its minimum energy surface structure, the probe spans a height

• . Computational simulations Geometry optimization, as well as frequency calculations for the flipper mechanophore, were performed in the gas phase at the density functional level of theory with the Gaussian 03 program package [35] using the hybrid B3LYP functional [36] in conjunction with the LanL2DZ basis set

Cycloheximide congeners produced by Streptomyces sp. SC0581 and photoinduced interconversion between (E)- and (Z)-2,3-dehydroanhydrocycloheximides

• Li Yang,
• Ping Wu,
• Jinghua Xue,
• Huitong Tan,
• Zheng Zhang and
• Xiaoyi Wei

Beilstein J. Org. Chem. 2017, 13, 1039–1049, doi:10.3762/bjoc.13.103

• . The column temperature was controlled at 40 °C and detection wavelength was set at 280 nm. Computational details Molecular Merck force field (MMFF) calculations were done using the Spartan'14 program (Wavefunction Inc., Irvine, CA, USA). Density functional theory (DFT) and time-dependent density

• functional theory (TDDFT) calculations were performed with the Gaussian 09 program package [24]. For computations of ECD spectra, the conformers generated by a MMFF conformational search in an energy window of 10 kcal/mol were subjected to geometry optimization using the dispersion-corrected DFT-D3 method

Conformational study of L-methionine and L-cysteine derivatives through quantum chemical calculations and ³J_HH coupling constant analyses

• Weslley G. D. P. Silva,
• Carolyne B. Braga and
• Roberto Rittner

Beilstein J. Org. Chem. 2017, 13, 925–937, doi:10.3762/bjoc.13.94

• calculations, such as the Møller–Plesset (MP2) method and density functional theory (DFT) calculations, together with experimental techniques have been combined to achieve more accurate results [20][21][22][23][24]. Some amino acid derivatives have been recently studied by our research group, including the

Molecular-level architectural design using benzothiadiazole-based polymers for photovoltaic applications

• Vinila N. Viswanathan,
• Arun D. Rao,
• Upendra K. Pandey,
• Arul Varman Kesavan and
• Praveen C. Ramamurthy

Beilstein J. Org. Chem. 2017, 13, 863–873, doi:10.3762/bjoc.13.87

• studied. The polymer, derived from dithienylated benzothiodiazole and fluorene, P1, exhibited a highest occupied molecular orbital (HOMO) energy level at −5.48 eV. Density functional theory (DFT) studies as well as experimental measurements suggested that upon substitution of the acceptor with fluorine

• stability with onset decomposition temperature of >410 °C. Computational modeling of the three polymers was performed to gain insight into the molecular energy levels along with band gaps using density functional theory (DFT) at the B3LYP/6-31G (d,p) level as implemented in Gaussian-09 software [37]. For

• bridge, a torsion angle of 179° is found between the benzothiadiazole and thienothiophene part. This clearly indicates an increased planarity of the polymer P3 compared to P1 due to the presence of the fused π-bridge. Moreover, time-dependent density functional theory (TDDFT) calculations were also

Continuous-flow processes for the catalytic partial hydrogenation reaction of alkynes

• Carmen Moreno-Marrodan,
• Francesca Liguori and
• Pierluigi Barbaro

Beilstein J. Org. Chem. 2017, 13, 734–754, doi:10.3762/bjoc.13.73

• selectivity trend was explained in terms of both adsorption mode on and relative accessibility to Pd active sites, depending on surface potentials and hindrance of modifiers, on the basis of density functional theory and molecular dynamics calculations. The rationale was summarized in the so-called

Spectral and DFT studies of anion bound organic receptors: Time dependent studies and logic gate applications

• Srikala Pangannaya,
• Neethu Padinchare Purayil,
• Shweta Dabhi,
• Venu Mankad,
• Prafulla K. Jha,
• Satyam Shinde and
• Darshak R. Trivedi

Beilstein J. Org. Chem. 2017, 13, 222–238, doi:10.3762/bjoc.13.25

• understand the binding mechanism, we have performed a density functional theory (DFT) simulation on the receptor molecules using the GAUSSIAN 09 software package [44]. A closed-shell Becke–Lee–Yang–Parr hybrid exchange–correlation three-parameter functional (B3LYP) [45] along with the 6-311++G(d,p) basis set

Self-optimisation and model-based design of experiments for developing a C–H activation flow process

• Alexander Echtermeyer,
• Yehia Amar,
• Jacek Zakrzewski and
• Alexei Lapkin

Beilstein J. Org. Chem. 2017, 13, 150–163, doi:10.3762/bjoc.13.18

• in self-optimisation and model-development frameworks is not well documented in the literature. Very recently we have shown that a priori knowledge in the form of density functional theory level (DFT) mechanistic calculations can be used to propose process models and to perform in silico design of

Characterization of the synthetic cannabinoid MDMB-CHMCZCA

• Carina Weber,
• Stefan Pusch,
• Dieter Schollmeyer,
• Sascha Münster-Müller,
• Michael Pütz and
• Till Opatz

Beilstein J. Org. Chem. 2016, 12, 2808–2815, doi:10.3762/bjoc.12.279

• CO and/or a cyclohexyl radical or methylenecyclohexane. As MDMB-CHMCZCA bears a stereogenic center at C-1', the elucidation of the absolute configuration of the sample was attempted by ECD spectroscopy. While the UV spectra can be adequately predicted by TD-DFT calculations (time-dependent density

• functional theory, see Supporting Information File 1 for details), a comparison of the experimental and calculated ECD spectra did not allow for a safe assignment of the cannabimimetic’s absolute configuration (Figure 4). The main two positive ECD signals in the range above 230 nm are correctly predicted by

Effects of solvent additive on “s-shaped” curves in solution-processed small molecule solar cells

• John A. Love,
• Shu-Hua Chou,
• Ye Huang,
• Guilllermo C. Bazan and
• Thuc-Quyen Nguyen

Beilstein J. Org. Chem. 2016, 12, 2543–2555, doi:10.3762/bjoc.12.249

• measured to be 32 mg/mL for p-SIDT(FBTThCA8)2 compared with over 50 mg/mL for p-SIDT(FBTTh2)2 in chloroform at room temperature. Frontier molecular energy levels were estimated by cyclic voltammograms (CV) in dichloromethane and calculated theoretically by density functional theory (DFT) (Supporting

High performance p-type molecular electron donors for OPV applications via alkylthiophene catenation chromophore extension

• Paul B. Geraghty,
• Calvin Lee,
• Jegadesan Subbiah,
• Wallace W. H. Wong,
• James L. Banal,
• Mohammed A. Jameel,
• Trevor A. Smith and
• David J. Jones

Beilstein J. Org. Chem. 2016, 12, 2298–2314, doi:10.3762/bjoc.12.223

• and overlap, density functional theory (DFT) calculations were performed. Geometry optimization and molecular orbital surfaces were determined and are shown in Figure 11. Geometries of the BXR series were obtained at the D2 dispersion corrected B3LYP/6-311G(d,p) level of theory. Subsequent time