Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• bacterial sugars, the parametrisation of each building block is needed and requires the use of ab initio methodologies, including several steps of charges and electron density calculations, optimization and minimization, making the computational study of bacterial glycans difficult and time-consuming. 2

• , modifications can sometimes be required and can be achieved through ab initio calculations or programs like for example VFFDT [71]. Tools for the conformational analysis of glycans in the free state The structure and biological functions of glycans are closely intertwined; the roles they play are influenced not

• angles, bond length and bond angles), distance constraints (according to laws of physics) and gives an output with the structure with the minimised energy (https://alphafold.ebi.ac.uk/). 2. I-TASSER [89]: Iterative Threading ASSEmbly Refinement is a free online server that combines ab initio protein

Novel route to enhance the thermo-optical performance of bicyclic diene photoswitches for solar thermal batteries

• Akanksha Ashok Sangolkar,
• Rama Krishna Kadiyam and
• Ravinder Pawar

Beilstein J. Org. Chem. 2024, 20, 1053–1068, doi:10.3762/bjoc.20.93

• generated. The thermal stability and reversibility of the photoswitching cycle of the type-IIa photoswitch was analyzed using the ab initio molecular dynamics (AIMD) simulations. The proposed mechanism for the thermal back conversion and undesired thermal degradation of the photoproduct is illustrated in

• expected local minima on the PES. To confirm the reversible photoswitching in the studied BBD-based switches, ab initio molecular dynamics (AIMD) simulations were carried out. The simulations were initiated using the singlet biradicaloid TS of the IIa photoswitch. The simulations were performed for 2 ps

Photochromic derivatives of indigo: historical overview of development, challenges and applications

• Gökhan Kaplan,
• Zeynel Seferoğlu and
• Daria V. Berdnikova

Beilstein J. Org. Chem. 2024, 20, 228–242, doi:10.3762/bjoc.20.23

• the O atom (Figure 6b). Moreover, the data of the first systematic computational ab initio study of the molecular mechanism of the photostability of indigo [36] support these findings and additionally point out that the single proton transfer (SPT) is more favorable than the double proton transfer

Strategies to access the [5-8] bicyclic core encountered in the sesquiterpene, diterpene and sesterterpene series

• Cécile Alleman,
• Charlène Gadais,
• Laurent Legentil and
• François-Hugues Porée

Beilstein J. Org. Chem. 2023, 19, 245–281, doi:10.3762/bjoc.19.23

Mechanochemical bottom-up synthesis of phosphorus-linked, heptazine-based carbon nitrides using sodium phosphide

• Blaine G. Fiss,
• Georgia Douglas,
• Michael Ferguson,
• Jorge Becerra,
• Jesus Valdez,
• Trong-On Do,
• Tomislav Friščić and
• Audrey Moores

Beilstein J. Org. Chem. 2022, 18, 1203–1209, doi:10.3762/bjoc.18.125

• previous work [38] of substituting bridging nitrogen atoms for phosphorus in previously reported heptazine-based graphitic carbon nitrides. We adapted the ab initio predicted structures for a network of corrugated sheets [46] (Figure 4a and 4b) and planar sheets (Figure 4c) [47]. Additionally, we modelled

• calculated 31P chemical shifts at 37.7 ppm (P1) and 23.3 ppm (P2), respectively, while that of the paddlewheel monomer is at 11.2 ppm (P3). The calculated shifts demonstrate phosphorus environments in the mechanochemically synthesized material are distinct to those calculated in ab initio predicted models of

Double-headed nucleosides: Synthesis and applications

• Vineet Verma,
• Jyotirmoy Maity,
• Vipin K. Maikhuri,
• Ritika Sharma,
• Himal K. Ganguly and
• Ashok K. Prasad

Beilstein J. Org. Chem. 2021, 17, 1392–1439, doi:10.3762/bjoc.17.98

Structural effects of meso-halogenation on porphyrins

• Keith J. Flanagan,
• Maximilian Paradiz Dominguez,
• Zoi Melissari,
• Hans-Georg Eckhardt,
• René M. Williams,
• Dáire Gibbons,
• Caroline Prior,
• Gemma M. Locke,
• Alina Meindl,
• Aoife A. Ryan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2021, 17, 1149–1170, doi:10.3762/bjoc.17.88

• present are a current limitation. To combat this, we decided to expand these series with ab-initio computational molecular modelling. We focused on the structural modelling of three series. The ground-state geometries of several members of these series were optimized at the wB97-XD/cc-pVDZ level of theory

Metal-free glycosylation with glycosyl fluorides in liquid SO₂

• Krista Gulbe,
• Jevgeņija Lugiņina,
• Edijs Jansons,
• Artis Kinens and
• Māris Turks

Beilstein J. Org. Chem. 2021, 17, 964–976, doi:10.3762/bjoc.17.78

• stabilize the oxocarbenium ion formed from glycosyl perchlorate that is generated in situ from glycosyl chloride and AgClO4 [56]. Apart from that, SO2 has considerable affinity to the Lewis basic halide ions [57][58][59]. Kuhn et al. [60] and later Eisfield and Regitz [61] have published ab initio studies

CF₃-substituted carbocations: underexploited intermediates with great potential in modern synthetic chemistry

• Anthony J. Fernandes,
• Armen Panossian,
• Bastien Michelet,
• Agnès Martin-Mingot,
• Frédéric R. Leroux and
• Sébastien Thibaudeau

Beilstein J. Org. Chem. 2021, 17, 343–378, doi:10.3762/bjoc.17.32

• certain extent upon the electron demand in the system to which it is attached”. Thus, despite the strong intrinsic electron-withdrawing character, the trifluoromethyl group was shown to modestly act as a π-electron donor when substituting a carbenium ion. Ab initio calculations were performed to account

• alkylcarbenium ions, in which a higher electronic contribution from neighboring substituents is required. Detailed ab initio studies have been focused on the stability of the CF3CH2+ cation and provide pieces of thoughts on the origins of the stabilizing interactions in α-(trifluoromethyl)carbenium ions. The

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

• Carl A. Fogarty,
• Aoife M. Harbison,
• Amy R. Dugdale and
• Elisa Fadda

Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171

• is able to form when in a 1C4 chair with the α(1-6)-Man, which may compensate for the steric compression, making the 1C4 chair the highest populated conformer at 76% within an N-glycan scaffold. Both experimental and ab-initio theoretical studies [36][37][38] have shown that the 1C4 chair is

Models of necessity

• Timothy Clark and
• Martin G. Hicks

Beilstein J. Org. Chem. 2020, 16, 1649–1661, doi:10.3762/bjoc.16.137

• calculations use very space-extensive atomic orbitals (AOs, basis functions) that extend into the neighborhood of adjacent atoms (however that is defined). This problem manifests itself concretely as basis-set superposition error (BSSE) [21] in ab initio calculations but rears its ugly head in every AO-based

p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies

• Panagiotis S. Gritzapis,
• Panayiotis C. Varras,
• Nikolaos-Panagiotis Andreou,
• Katerina R. Katsani,
• Konstantinos Dafnopoulos,
• George Psomas,
• Zisis V. Peitsinis,
• Alexandros E. Koumbis and
• Konstantina C. Fylaktakidou

Beilstein J. Org. Chem. 2020, 16, 337–350, doi:10.3762/bjoc.16.33

• ) Optimized structures of compounds 25–27 with the ab initio DFT computational methods, 4) DNA binding studies; 5) UV absorption spectra of all amidoxime, ethanone oxime and aldoxime carbamates; 6) Gel electrophoresis pictures of all amidoxime, ethanone oxime and aldoxime carbamate; 7) UV absorption spectra

Combination of multicomponent KA² and Pauson–Khand reactions: short synthesis of spirocyclic pyrrolocyclopentenones

• Riccardo Innocenti,
• Elena Lenci,
• Gloria Menchi and
• Andrea Trabocchi

Beilstein J. Org. Chem. 2020, 16, 200–211, doi:10.3762/bjoc.16.23

• subjected to ab initio single point energy calculation at the 3-21G*/ HF level of quantum chemical theory. PCA analysis. The web-based public tool ChemGPS-NP was used for PCA analysis of compounds 3–39, to compare their chemical properties with those of blockbuster drugs. ChemGPS-NP can be applied for

• rod, disc and sphere, respectively. Chemical structure of representative approved drugs containing a spirocyclic moiety. Top: Selected NOE contacts from NOESY 1D spectra of compound 36; bottom: low energy conformer of 36, Z rotamer, using ab initio calculation at the HF/3-21G* level. PCA plot

An overview of the cycloaddition chemistry of fulvenes and emerging applications

• Ellen Swan,
• Kirsten Platts and
• Anton Blencowe

Beilstein J. Org. Chem. 2019, 15, 2113–2132, doi:10.3762/bjoc.15.209

• ) through bond rotation [30][61][62][70]. Furthermore, the nature of the substituents on the exocyclic carbon influences the fulvene reactivity and stability (Scheme 2) [30][42][48][52][53][54][64][67][69][71]. An ab initio study by Krygowski et al. [15] reported that pentafulvene derivatives (not aromatic

Cyclobutane dication, (CH₂)₄²⁺: a model for a two-electron four-center (2e-4c) Woodward–Hoffmann frozen transition state

• G. K. Surya Prakash and
• Golam Rasul

Beilstein J. Org. Chem. 2019, 15, 1475–1479, doi:10.3762/bjoc.15.148

• the potential energy surface (PES) of H42+. The structure of the rectangular shaped cyclobutane dication (CH2)42+ (vi) was computed by Olah, Prakash et al. [8][10] using semiempirical and ab initio methods and later by Herges, von Ragué Schleyer, Schindler and Fessner [11] using an ab initio method

Influence of per-O-sulfation upon the conformational behaviour of common furanosides

• Alexey G. Gerbst,
• Vadim B. Krylov,
• Dmitry A. Argunov,
• Maksim I. Petruk,
• Arsenii S. Solovev,
• Andrey S. Dmitrenok and
• Nikolay E. Nifantiev

Beilstein J. Org. Chem. 2019, 15, 685–694, doi:10.3762/bjoc.15.63

• and β-galactose. Full exploration of the furanoside ring by means of ab initio calculations was performed and coupling constants were calculated for each of the low-energy conformers. The results demonstrated preferred trans-orientation of H4–H5 protons in the non-sulfated molecules which changed to

• of sulfates. Keywords: ab initio calculations; conformational analysis; furanosides; NMR; sulfation; Introduction Changes in the conformations of monosaccharides expectedly accompany their modification with different functional groups. Thus, spatial repulsion of silyl groups results in inversion or

• : O4–C1–O1–CH2 torsion was set to +60° or −60° depending on α- or β-configuration of the sugar in accordance with the exo-anomeric effect. Other starting torsions in the propyl group had trans-orientation. Geometry optimizations of all the thus obtained structures were carried out at ab initio HF/6-311

Conformational signature of Ishikawa´s reagent using NMR information from diastereotopic fluorines

• Laize A. F. Andrade,
• Lucas A. Zeoly,
• Rodrigo A. Cormanich and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2019, 15, 506–512, doi:10.3762/bjoc.15.44

• DFT results are also consistent with ab initio MP2 electronic energies (Supporting Information File 1). Opposite to the expectation of a double fluorine gauche effect (σC–H/C–C → σ*C–F) [19][20][21][22][23] as ruling mechanism of the conformational stability of 1, the 1Ab conformer appears as the main

Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA

• Sibylle Frei,
• Adam K. Katolik and
• Christian J. Leumann

Beilstein J. Org. Chem. 2019, 15, 79–88, doi:10.3762/bjoc.15.9

• oligonucleotides hybridized to RNA showed a similar structure than the natural DNA/RNA duplex. Furthermore, since the structural investigation on the nucleoside level by X-ray crystallography and ab initio calculations pointed to a furanose conformation in the southern region, a RNase H cleavage assay was

Dispersion-mediated steering of organic adsorbates on a precovered silicon surface

• Lisa Pecher,
• Sebastian Schmidt and
• Ralf Tonner

Beilstein J. Org. Chem. 2018, 14, 2715–2721, doi:10.3762/bjoc.14.249

• formed. The results show that dispersive interactions can be decisive in building novel organic structures on surfaces by tweaking the potential energy surface. Computational Details All calculations were performed with the Vienna Ab Initio Simulation Package (VASP) [12][13][14][15] version 5.3.5 using

• observation of nonstatistical chain formation can thus be explained. Especially for larger adsorbates, these attractive interactions are expected to play an important role in determining the surface arrangement of molecules and might thus be even used for designing patterned surfaces. To this end, ab initio

Design, synthesis and structure of novel G-2 melamine-based dendrimers incorporating 4-(n-octyloxy)aniline as a peripheral unit

• Cristina Morar,
• Pedro Lameiras,
• Attila Bende,
• Gabriel Katona,
• Emese Gál and
• Mircea Darabantu

Beilstein J. Org. Chem. 2018, 14, 1704–1722, doi:10.3762/bjoc.14.145

• block copolymers and G-0 monomeric or dimeric dendritic liquid crystals with photochromic azobenzene mesogens. The present ab initio study explores a previously unknown use of 4-(n-octyloxy)aniline in the synthesis, structure and supramolecular behaviour of new dendritic melamines. Results: Starting

• frameworks) [35]. All the above information prompted us towards an ab initio exploration of 4-(n-octyloxy)aniline (seen as the n-octyl ether derivative of 4-aminophenol) as starting material towards new melamine-based dendrimers as synthesis (feasibility and limits), structure and self-assembly propensity

• ) promoted, as in the case of 7b, by the same arched G-1 branches. 3.4 Assignments by means of TEM analyses We also considered of interest to corroborate our ab initio study with an introductory exploration by means of TEM (transmission electronic microscopy). In this purpose, the sampling was made by

Correlation effects and many-body interactions in water clusters

• Andreas Heßelmann

Beilstein J. Org. Chem. 2018, 14, 979–991, doi:10.3762/bjoc.14.83

• methods on an adequate level, e.g., random-phase approximation electron correlation methods. The relative magnitudes of the different interaction energy contributions obtained by accurate ab initio calculations can therefore provide useful insights that can be exploited to develop enhanced force field

• . These commonly depend on a number of empirical parameters that are determined either by a fit to experimentally known liquid or bulk properties, or by fitting to energies from ab initio quantum chemistry methods. The most popular potentials for water are the TIP3P [2], TIP4P [2][3] and TIP5P [4][5

• ] force fields, which are based on a modeling of the water pair potential using an electrostatic contribution described by interacting point charges and a van der Waals interaction contribution using Lennard-Jones potentials. In more advanced ab initio water pair potentials the force field is fitted to

A permutation approach to the assignment of the configuration to diastereomeric tetrads by comparison of experimental and ab initio calculated differences in NMR data

• Przemysław J. Boratyński

Beilstein J. Org. Chem. 2017, 13, 2478–2485, doi:10.3762/bjoc.13.245

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

• tendency while studying a series of substituents at the 5-position of tetrazolo[1,5-a]pyridines using ab initio calculations. Their findings indicated that electron-withdrawing groups stabilize the azide isomer while electron-donating groups stabilize the tetrazole ring. Additionally, it was observed that

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

• different energy minima were identified for 1 and 2, respectively. The 34 geometries of 2 were fully reoptimized without restrictions using the B3LYP [34][35], B3LYP-D3 [36], CAM-B3LYP [37], M05-2X [38], M06-2X [39], B97-D [40] and ωB97X-D [41] functionals, and the ab initio MP2 method [42], with the aug-cc

Derivatives of the triaminoguanidinium ion, 5. Acylation of triaminoguanidines leading to symmetrical tris(acylamino)guanidines and mesoionic 1,2,4-triazolium-3-aminides

• Jan Szabo,
• Julian Greiner and
• Gerhard Maas

Beilstein J. Org. Chem. 2017, 13, 579–588, doi:10.3762/bjoc.13.57

• geometry of the parent 1,2,4-triazolium-3-aminide has been calculated by quantum chemical ab initio methods [40]. The bond length differences are in qualitative agreement with the experimentally determined values for 7a. On protonation or methylation of the exocyclic aminide nitrogen atom, the mesoionic

• 1,2,4-triazolium-3-aminides 7a–e, the chemical shifts of ring atoms C-3 and C-5 are of interest (Table 3; for ab initio GIAO-CHF calculations of chemical shifts of the parent 1,2,4-triazolium-3-aminide, see lit. [40]). The C-3 chemical shifts of 7a–e are equal within 1.14 ppm and are in the typical