Oxidation of [3]naphthylenes to cations and dications converts local paratropicity into global diatropicity

• Abel Cárdenas,
• Zexin Jin,
• Yong Ni,
• Jishan Wu,
• Yan Xia,
• Francisco Javier Ramírez and
• Juan Casado

Beilstein J. Org. Chem. 2025, 21, 277–285, doi:10.3762/bjoc.21.20

• bonding changes. Stretching force constants were evaluated to monitor the aromatic–antiaromatic alternation pattern upon oxidation. They showed us that the dication of linear [3]naphthylene became an overall global π-electron delocalized molecule. This result was supported by nucleus independent chemical

• shift (NICS) calculations and anisotropy of the current induced density (ACID) plots, as they evidenced the presence of a perimetral diatropic global ring current upon oxidation. Keywords: ACID; aromaticity; force constants; NICS; spectroscopy; Introduction Since the discovery of conjugated polymers

• is using energetic parameters unequivocally associated to individual bonds. This is the case of the vibrational force constants [22]. They are defined as the second derivative of the molecular energy, in the minimum energy molecular structure, with respect to the nuclear displacement coordinates

Improving the accuracy of ³¹P NMR chemical shift calculations by use of scaling methods

• William H. Hersh and
• Tsz-Yeung Chan

Beilstein J. Org. Chem. 2023, 19, 36–56, doi:10.3762/bjoc.19.4

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• a time step of 0.001 ps. The particle mesh Ewald (PME) method was used. Nonbonded interactions were cut-off using the force-switching method from 10 Å to 12 Å, and hydrogen bonding constraints applied. During equilibration, the protein backbone and side chains were restrained (force constants of

Metal-mediated base pairs in parallel-stranded DNA

• Jens Müller

Beilstein J. Org. Chem. 2017, 13, 2671–2681, doi:10.3762/bjoc.13.265

• represents a local energy minimum rather than the global one. In the structure shown in Scheme 9c, all Hg···N and Hg···O force constants amount to ≈2 N cm−1 and hence indicate strong bonds [80]. The fourfold positive charge of the two Hg(II) ions in the εA–Hg(II)2–T base pair is stabilized by three factors

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

• followed by recording infrared spectra [16][17][18][19][20][21][22][23][24][25][26][27][28][29]. External force modifies the force constants of vibrational modes [30]. Since structural deformation changes the charge distribution in the molecule, the transition dipole moment and thus the infrared intensity

Methylenelactide: vinyl polymerization and spatial reactivity effects

• Judita Britner and
• Helmut Ritter

Beilstein J. Org. Chem. 2016, 12, 2378–2389, doi:10.3762/bjoc.12.232

• of the force constants of the C–H bonds on a DFT level. The C–H stretching vibrations ν(C-H) = 2948 cm−1 of poly(MLA) determined via IR spectroscopy correlate well with the force constant of k = 473 N m−1 (calculations see Figure S6, Supporting Information File 1). In contrast, the monomer MLA (ν(C-H

Correction: Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

• Jörg Grunenberg and
• Giuseppe Licari

Beilstein J. Org. Chem. 2016, 12, 608–610, doi:10.3762/bjoc.12.59

• ; computational chemistry; drug design; molecular recognition; relaxed force constants; Our original publication contains an erratic number of predicted antibiotic structures in Scheme 2. With this Erratum we provide the corrected Scheme 2. Scheme 2 in the original article: Predicted new linezolid-like

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

• Jörg Grunenberg and
• Giuseppe Licari

Beilstein J. Org. Chem. 2016, 12, 415–428, doi:10.3762/bjoc.12.45

• , followed by an evaluation of their enthalpic penalties or rewards and the mechanical strengths of the relevant hydrogen bonds (relaxed force constants; compliance constants). The protocol was able to reproduce the experimentally known enantioselectivity favoring the S-enantiomer. In a second step, the

• : compliance constants; computational chemistry; drug design; molecular recognition; relaxed force constants; Introduction Antibiotic resistance is one of the major health problems in modern societies, causing millions of deaths per year [1][2][3]. Although Alexander Fleming recognized the importance of the

Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis

• Stephanie R. Hare and
• Dean J. Tantillo

Beilstein J. Org. Chem. 2016, 12, 377–390, doi:10.3762/bjoc.12.41

• capable of ab initio or density functional theory (DFT) calculations is used to calculate either (1) force constants (via frequency calculation) along the trajectory, either at every point or in periodic increments, or (2) the gradient of the potential energy, depending on the specific integrator chosen

• to integrate the equations of motion. The calculation of gradients rather than force constants is significantly faster, but requires a smaller time step to achieve the same calculation accuracy. The calculations are run under the Born–Oppenheimer Approximation, which is why they are also called Born

• calculate force constants. For a 1 ps long direct dynamics trajectory with a time step of 1 fs where force constants are calculated at each point, the nuclear and electronic structure of the molecule will need to be recalculated a total of 1000 times, which equates to a great deal of computer time, even in

Biantennary oligoglycines and glyco-oligoglycines self-associating in aqueous medium

• Svetlana V. Tsygankova,
• Alexander A. Chinarev,
• Alexander B. Tuzikov,
• Nikolai Severin,
• Alexey A. Kalachev,
• Juergen P. Rabe,
• Alexandra S. Gambaryan and
• Nicolai V. Bovin

Beilstein J. Org. Chem. 2014, 10, 1372–1382, doi:10.3762/bjoc.10.140

• (Digital Instruments, USA). Commercial silicon nitride cantilevers with force constants of 0.06, 0.12, and 0.32 Nm−1 were used for the measurements in contact mode in liquid cell. Cantilevers with a resonance frequency of about 300 kHz and a force constant of 42 Nm−1 were used for the SFM tapping mode in

Substrate dependent reaction channels of the Wolff–Kishner reduction reaction: A theoretical study

• Shinichi Yamabe,
• Guixiang Zeng,
• Wei Guan and
• Shigeyoshi Sakaki

Beilstein J. Org. Chem. 2014, 10, 259–270, doi:10.3762/bjoc.10.21

• optimization in the first step, a full optimization of the TS was carried out by the use of the Hessian force constant matrices in the second step. To the Cl···C and C···Br distances, negative force constants were specified to obtain the TS geometry of the bond interchange C–Br → Cl–C. TSs were characterized

Electron self-exchange activation parameters of diethyl sulfide and tetrahydrothiophene

• Martin Goez and
• Martin Vogtherr

Beilstein J. Org. Chem. 2013, 9, 1448–1454, doi:10.3762/bjoc.9.164

• λi), as well as rearranging the solvent shell to accommodate the charge distribution of the respective other side of the reaction equation (outer reorganization energy λ0). In the majority of cases, λi, which is usually calculated from the force constants and geometry differences of the reactants [1

Photoionisation of the tropyl radical

• Kathrin H. Fischer,
• Patrick Hemberger,
• Andras Bodi and
• Ingo Fischer

Beilstein J. Org. Chem. 2013, 9, 681–688, doi:10.3762/bjoc.9.77

• radical. We employed the geometry, frequencies and force constants of the CASSCF calculation from Stakhursky et al. [13] in the simulation. Note that their work accurately describes the Jahn–Teller distortion and thus represents the best available description of the radical potential-energy surface. They

Caryolene-forming carbocation rearrangements

• Quynh Nhu N. Nguyen and
• Dean J. Tantillo

Beilstein J. Org. Chem. 2013, 9, 323–331, doi:10.3762/bjoc.9.37

• with B3LYP/6-31G(d) [68][69][70][71][72]. For IRC calculations, force constants were recalculated after every three points or at every point in the event of prematurely terminated jobs. All molecules were then subjected to optimization and frequency calculations at the B3LYP/6-31+G(d,p) level of theory