Peptide models XXXI. Conformational properties of hydrophobic residues shaping the core of proteins. An ab initio study of N‐formyl‐L‐valinamide and N‐formyl‐L‐phenylalaninamide

Employing introductory (3‐21G RHF) and medium‐size (6‐311++G** B3LYP) ab initio calculations, complete conformational libraries, containing as many as 27 conformers, have been determined for diamide model systems incorporating the amino acids valine (Val) and phenylalanine (Phe). Conformational and energetic properties of these libraries were analyzed. For example, significant correlation was found between relative energies from 6‐311++G** B3LYP and single‐point B3LYP/6‐311++G**//RHF/3‐21G calculations. Comparison of populations of molecular conformations of hydrophobic aromatic and nonaromatic residues, based on their ab initiorelative energies, with their natural abundance indicates that, at least for the hydrophobic core of proteins, the conformations of Val (Ile, Leu) and Phe (Tyr, Trp) are controlled by the local energetic preferences of the respective amino acids. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 732–751, 2001     

Conformational analysis,part 43. A theoretical and LIS/NMR investigation of the conformations of substituted benzamides

A refined Lanthanide‐Induced‐Shift Analysis (LISA) is used with molecular mechanics and ab initio calculations to investigate the conformations of benzamide ( 1 ), N‐methylbenzamide ( 2 ), N,N‐dimethylbenzamide ( 3 ) and the conformational equilibria of 2‐fluoro ( 4 ), 2‐chloro ( 5 ) and N‐methyl‐2‐methoxy benzamide ( 6 ). The amino group in 1 is planar in the crystal but is calculated to be pyramidal with the CO/phenyl torsional angle (ω) of 20–25°. The LISA analysis gave acceptable agreement factors (Rcryst ≤ 1%) for the ab initio geometries when ω was decreased to 0°, the other geometries were not as good. In 2 , the N‐methyl is coplanar with the carbonyl group in all the geometries. Good agreement was obtained for the RHF geometries, with ω 25°, the other geometries were only acceptable with increased values of ω. In 3 , good agreement for the RHF and PCModel geometries was found when ω was changed from the calculated values of 40° (RHF) and 90° (PCModel) to ca. 60°, the X‐ray and B3LYP geometries were not as good. The two substituted compounds 4 , 5 and 6 are interconverting between the cis (O,X) and trans (O,X) conformers. The more stable trans conformer is planar in 4 and 6 but the cis form non‐planar. Both the cis and trans conformers of 5 are non‐planar. There is an additional degree of freedom in 6 due to the 2‐methoxy group, which can be either planar or orthogonal to the phenyl ring in both conformers. The conformer ratios were obtained from the LISA analysis to give Ecis‐Etrans in 4 > 2.3 kcal/mol (CDCl₃) and 1.7 kcal/mol (CD₃CN), in 5 0.0 kcal/mol (CD₃CN) and in 6 > 2.5 kcal/mol (CDCl₃) and 2.0 kcal/mol (CD₃CN). These values were used with the observed versus calculated ¹H shifts to determine the conformer ratios and energies in DMSO solvent to give Ecis‐Etrans 1.1, ?0.1 and 1.8 kcal/mol for ( 4 ), ( 5 ) and ( 6 ). Comparison of the observed versus calculated conformer energies show that both the MM and ab initio calculations overestimate the NH..F hydrogen bond in ( 4 ) by ca. 2 kcal/mol. Copyright © 2015 John Wiley & Sons, Ltd.     

1H, 13C, 17O NMR and quantum‐chemical study of the stereochemistry of the sulfoxide and sulfone derivatives of 3‐arylidene‐1‐thioflavan‐4‐one epoxides

The oxidation of the trans,cis‐( 2 ) and trans,trans‐epoxides ( 3 ) of differently substituted (Z)‐3‐arylidene‐1‐thioflavan‐4‐ones ( 1 ) with dimethyldioxirane (DMD) yielded the appropriate sulfoxides ( 4, 5 ) and sulfones ( 6, 7 ). The structures were elucidated by the extensive application of one‐ and two‐dimensional ¹H, ¹³C and ¹⁷O NMR spectroscopy. The conformational analysis was achieved by the application of ³J(C,H) coupling constants, NOESY responses and ab initio calculations. The preferred ground‐state conformers (twisted envelope‐A, twisted envelope‐B for 6 and twisted envelope‐A, envelope‐B for 7 ) were obtained as global minima of the theoretical ab initio MO study and also the examination of the ¹⁷O and ¹³C chemical shifts, calculated for the global minima structures of the sulfone isomers by the GIAO method. Analogous results, obtained for the sulfoxide isomers ( 4, 5 ), not only led to the preferred conformers but also gave evidence for the trans arrangement of the 2‐Ph group and the oxygen atom of the S?O group. Chemical shift differences between the isomers, sulfoxides and sulfones were corroborated by ab initio calculations of the anisotropic effects of the oxirane ring and the S?O and SO₂ groups. Copyright © 2003 John Wiley & Sons, Ltd.     

Toward direct determination of conformations of protein building units from multidimensional NMR experiments I. A theoretical case study of For‐Gly‐NH2 and For‐L‐Ala‐NH2

NMR chemical shielding anisotropy tensors have been computed, employing several basis sets and the GIAO‐RHF and GIAO‐MP2 formalisms of electronic structure theory, for all the atoms of the five and nine typical backbone conformers of For‐Gly‐NH₂ and For‐L ‐Ala‐NH₂, respectively. Multidimensional chemical shift plots, as a function of the respective backbone fold, have been generated for both peptide models. On the 2D ¹H^NH‐¹⁵N^NH and ¹⁵N^NH‐¹³C^α plots the most notable feature is that at all levels of theory studied the backbone conformers cluster in different regions. Computed chemical shifts, as well as their averages, have been compared to relevant experimental values taken from the BioMagnetic Resonance Bank (BMRB). At the highest levels of theory, for all nuclei but the amide protons, deviations between statistically averaged theoretical and experimental shifts are as low as 1–3%. These results indicate that chemical shift information from selected multiple‐pulse NMR experiments (e.g., 2D‐HSQC and 3D‐HNCA) could directly be employed to extract folding information for polypeptides and proteins. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 882–900, 2000     

Synthesis and Conformational Analysis of 1′‐ and 3′‐Substituted 2‐Deoxy‐2‐fluoro‐D‐ribofuranosyl Nucleosides

Convergent syntheses of the 9‐(3‐X‐2,3‐dideoxy‐2‐fluoro‐β‐D ‐ribofuranosyl)adenines 5 (X=N₃) and 7 (X=NH₂), as well as of their respective α‐anomers 6 and 8 , are described, using methyl 2‐azido‐5‐O‐benzoyl‐2,3‐dideoxy‐2‐fluoro‐β‐D ‐ribofuranoside ( 4 ) as glycosylating agent. Methyl 5‐O‐benzoyl‐2,3‐dideoxy‐2,3‐difluoro‐β‐D ‐ribofuranoside ( 12 ) was prepared starting from two precursors, and coupled with silylated N⁶‐benzoyladenine to afford, after deprotection, 2′,3′‐dideoxy‐2′,3′‐difluoroadenosine ( 13 ). Condensation of 1‐O‐acetyl‐3,5‐di‐O‐benzoyl‐2‐deoxy‐2‐fluoro‐β‐D ‐ribofuranose ( 14 ) with silylated N²‐palmitoylguanine gave, after chromatographic separation and deacylation, the N⁷‐β‐anomer 17 as the main product, along with 2′‐deoxy‐2′‐fluoroguanosine ( 15 ) and its N⁹‐α‐anomer 16 in a ratio of ca. 42 : 24 : 10. An in‐depth conformational analysis of a number of 2,3‐dideoxy‐2‐fluoro‐3‐X‐D ‐ribofuranosides (X=F, N₃, NH₂, H) as well as of purine and pyrimidine 2‐deoxy‐2‐fluoro‐D ‐ribofuranosyl nucleosides was performed using the PSEUROT (version 6.3) software in combination with NMR studies.     

Indirect reversed‐phase high‐performance liquid chromatographic and direct thin‐layer chromatographic enantioresolution of (R,S)‐Cinacalcet

Enantioresolution of the calcimimetic drug (R,S)‐Cinacalcet was achieved using both indirect and direct approaches. Six chiral variants of Marfey's reagent having l ‐Ala‐NH₂, l ‐Phe‐NH₂, l ‐Val‐NH₂, l ‐Leu‐NH₂, l ‐Met‐NH₂ and d ‐Phg‐NH₂ as chiral auxiliaries were used as derivatizing reagents under microwave irradiation. Derivatization conditions were optimized. Reversed‐phase high‐performance liquid chromatography was successful using binary mixtures of aqueous trifluoroacetic acid and acetonitrile for separation of diastereomeric pairs with detection at 340 nm. Thin silica gel layers impregnated with optically pure l ‐histidine and l ‐arginine were used for direct resolution of enantiomers. The limit of detection was found to be 60 pmol in HPLC while in TLC it was found to be in the range of 0.26–0.28 µg for each enantiomers. Copyright © 2010 John Wiley & Sons, Ltd.     

Conformational Relaxation of p‐Phenylenevinylene Trimers in Solution Studied by Picosecond Time‐Resolved Fluorescence

Two p‐phenylenevinylene (PV) trimers, containing 3′‐methylbutyloxyl (in MBOPV3) and 2′‐ethylhexyloxyl (in EHOPV3) side chains, are used as model compounds of PV‐based conjugated polymers (PPV) with the purpose of clarifying the origin of fast (picosecond time) components observed in the fluorescence decays of poly[2‐methoxy‐5‐(2′‐ethylhexyloxy)‐p‐phenylenevinylene] (MEH‐PPV). The fluorescence decays of MBOPV3 and EHOPV3 reveal the presence of similar fast components, which are assigned to excited‐state conformational relaxation of the initial population of non‐planar trimer conformers to lower‐energy, more planar conformers. The rate constant of conformational relaxation k_CR is dependent on solvent viscosity and temperature, according to the empirical relationship k_CR=aη_o^?α?exp(?αE_η/RT), where aη_o^?α is the frequency factor, η_o is the pre‐exponential coefficient of viscosity, E_η is the activation energy of viscous flow. The empirical parameter α, relating the solvent microscopic friction involved in the conformational change to the macroscopic solvent friction (α=1), depends on the side chain. The fast component in the fluorescence decays of MEH‐PPV polymers (PPVs), is assigned to resonance energy transfer from short to longer polymer segments. The present results call for revising this assignment/interpretation to account for the occurrence of conformational relaxation, concurrently with energy transfer, in PPVs.     

Glycosylated Star‐Shaped Conjugated Oligomers for Targeted Two‐Photon Fluorescence Imaging

A glucopyranose functionalized star‐shaped oligomer, N‐tris{4,4′,4′′‐[(1E)‐2‐(2‐{(E)‐2‐[4‐(benzo[d]thiazol‐2‐yl)phenyl]vinyl}‐9,9‐bis(6‐2‐amido‐2‐deoxy‐1‐thio‐β‐D ‐glucopyranose‐hexyl)‐9H‐fluoren‐7‐yl)vinyl]phenyl}phenylamine (TVFVBN‐S‐NH₂), is synthesized for two‐photon fluorescence imaging. In water, TVFVBN‐S‐NH₂ self‐assembles into nanoparticles with an average diameter of ～49 nm and shows a fluorescence quantum yield of 0.21. Two‐photon fluorescence measurements reveal that TVFVBN‐S‐NH₂ has a two‐photon absorption cross‐section of ～1100 GM at 780 nm in water. The active amine group on the glucopyranose moiety allows further functionalization of TVFVBN‐S‐NH₂ with folic acid to yield TVFVBN‐S‐NH₂FA with similar optical and physical properties as those for TVFVBN‐S‐NH₂. Cellular imaging studies reveal that TVFVBN‐S‐NH₂FA has increased uptake by MCF‐7 cells relative to that for TVFVBN‐S‐NH₂, due to specific interactions between folic acid and folate receptors on the MCF‐7 cell membrane. This study demonstrates the effectiveness of glycosylation as a molecular engineering strategy to yield water‐soluble materials with a large two‐photon absorption (TPA) cross‐section for targeted cancer‐cell imaging.     

Synthesis and characterization of macroinitiator‐amino terminated PEG and poly(γ‐benzyl‐L‐glutamate)‐PEO‐poly(γ‐benzyl‐L‐glutamate) triblock copolymer

Macroinitiator‐amino terminated poly(ethylene glycol) (PEG) (NH₂‐PEO‐NH₂) was prepared by converting both terminal hydroxyl groups of PEG to more reactive primary amino groups. The synthetic route involved reactions of chloridize, phthalimide and finally hydrazinolysis. Furthermore, poly(γ‐benzyl‐L ‐glutamate)‐poly(ethylene oxide)‐poly(γ‐benzyl‐L ‐glutamate) (PBLG‐PEO‐PBLG) triblock copolymer was synthesized by polymerization of γ‐benzyl‐L ‐glutamate N‐carboxyanhydride (Bz‐L‐GluNCA) using NH₂‐PEO‐NH₂ as macroinitiator. The resultant NH₂‐PEO‐NH₂ and triblock copolymer were characterized by FT‐IR, ¹H‐NMR and gel permeation chromatography (GPC) techniques. The results demonstrated that the degree of amination of the NH₂‐PEO‐NH₂ could be up to 1.95. The molecular weight of the PBLG‐PEO‐PBLG triblock copolymer could be adjusted easily by controlling the molar ratio of Bz‐L ‐Glu NCA to the macroinitiator NH₂‐PEO‐NH₂. Copyright © 2004 John Wiley & Sons, Ltd.     

Quantum-Chemical Study of the Adducts of Silicon Halides with Nitrogen-containing Donors: II.1 Calculation of a Donor-Acceptor Bond Energy. Complex trans-SiH4·2NH3

Structural and thermodynamic characteristics of the trans-SiH₄·2NH₃ adduct were obtained by ab initio and DFT (RHF and B3LYP) calculations. Scanning the potential energy surface (PES) of the com plex showed that its structure corresponds to a local minimum, whereas the global minimum corresponds to the free fragments. The energy of the silicon-nitrogen chemical bond was calculated with inclusion of fragment rearrangement energies and basis set superposition error. The procedure offered for calculating the Si-N bond energy was extended to adducts of silicon halides with ammonia. It was found that the energy of SiX₄ rearrangement contributes most to the energies of donor-acceptor bonds in mono- and diammoniates of silicon tetrahalides.     

Conformational analysis of the disaccharide methyl α‐d‐mannopyranosyl‐(1→3)‐2‐O‐acetyl‐β‐d‐mannopyranoside monohydrate

The crystal structure of methyl α‐d ‐mannopyranosyl‐(1→3)‐2‐O‐acetyl‐β‐d ‐mannopyranoside monohydrate, C₁₅H₂₆O₁₂·H₂O, ( II ), has been determined and the structural parameters for its constituent α‐d ‐mannopyranosyl residue compared with those for methyl α‐d ‐mannopyranoside. Mono‐O‐acetylation appears to promote the crystallization of ( II ), inferred from the difficulty in crystallizing methyl α‐d ‐mannopyranosyl‐(1→3)‐β‐d ‐mannopyranoside despite repeated attempts. The conformational properties of the O‐acetyl side chain in ( II ) are similar to those observed in recent studies of peracetylated mannose‐containing oligosaccharides, having a preferred geometry in which the C2—H2 bond eclipses the C=O bond of the acetyl group. The C2—O2 bond in ( II ) elongates by ～0.02 Å upon O‐acetylation. The phi (?) and psi (ψ) torsion angles that dictate the conformation of the internal O‐glycosidic linkage in ( II ) are similar to those determined recently in aqueous solution by NMR spectroscopy for unacetylated ( II ) using the statistical program MA′AT, with a greater disparity found for ψ (Δ = ～16°) than for ? (Δ = ～6°).     

5‐Ethynyl‐2′‐deoxycytidine: a DNA building block with a `clickable' side chain

The title compound [systematic name: 4‐amino‐1‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐5‐ethynylpyrimidin‐2(1H)‐one], C₁₁H₁₃N₃O₄, shows two conformations in the crystalline state. The N‐glycosylic bonds of both conformers adopt similar conformations, with χ = −149.2 (1)° for conformer (I‐1) and −151.4 (1)° for conformer (I‐2), both in the anti range. The sugar residue of (I‐1) shows a C2′‐endo envelope conformation (²E, S‐type), with P = 164.7 (1)° and τ_m = 36.9 (1)°, while (I‐2) shows a major C3′‐exo sugar pucker (C3′‐exo‐C2′‐endo, ₃T², S‐type), with P = 189.2 (1)° and τ_m = 33.3 (1)°. Both conformers participate in the formation of a layered three‐dimensional crystal structure with a chain‐like arrangement of the conformers. The ethynyl groups do not participate in hydrogen bonding, but are arranged in proximal positions.     

1,N6‐Etheno‐2′‐deoxytubercidin hemihydrate

The title compound [systematic name: 7‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐7H‐imidazo[1,2‐c]pyrrolo[2,3‐d]pyrimidine hemihydrate], 2C₁₃H₁₄N₄O₃·H₂O or (I)·0.5H₂O, shows two similar conformations in the asymmetric unit. These two conformers are connected through one water molecule by hydrogen bonds. The N‐glycosylic bonds of both conformers show an almost identical anti conformation with χ = −107.7 (2)° for conformer (I‐1) and −107.0 (2)° for conformer (I‐2). The sugar moiety adopts an unusual N‐type (C3′‐endo) sugar pucker for 2′‐deoxyribonucleosides, with P = 36.8 (2)° and τ_m = 40.6 (1)° for conformer (I‐1), and P = 34.5 (2)° and τ_m = 41.4 (1)° for conformer (I‐2). Both conformers and the solvent molecule participate in the formation of a three‐dimensional pattern with a `chain'‐like arrangement of the conformers. The structure is stabilized by intermolecular O—H...O and O—H...N hydrogen bonds, together with weak C—H...O contacts.     

Conformation and tautomerism of methoxy‐substituted 4‐phenyl‐4‐thiazoline‐2‐thiones: a combined crystallographic and ab initio investigation

4‐Phenyl‐4‐thiazoline‐2‐thiol is an active pharmaceutical compound, one of whose activities is as a human indolenamine dioxygenase inhibitor. It has been shown recently that in both the solid state and the gas phase, the thiazolinethione tautomer should be preferred. As part of both research on this lead compound and a medicinal chemistry program, a series of substituted arylthiazolinethiones have been synthesized. The molecular conformations and tautomerism of 4‐(2‐methoxyphenyl)‐4‐thiazoline‐2‐thione and 4‐(4‐methoxyphenyl)‐4‐thiazoline‐2‐thione, both C₁₀H₉NOS₂, are reported and compared with the geometry deduced from ab initio calculations [PBE/6‐311G(d,p)]. Both the crystal structure analyses and the calculations establish the thione tautomer for the two substituted arylthiazolinethiones. In the crystal structure of the 2‐methoxyphenyl regioisomer, the thiazolinethione unit was disordered over two conformations. Both isomers exhibit similar hydrogen‐bond patterns [R₂²(8) motif] and form dimers. The crystal packing is further reinforced by short S…S interactions in the 2‐methoxyphenyl isomer. The conformations of the two regioisomers correspond to stable geometries calculated from an ab initio energy‐relaxed scan.     

A dual‐level direct dynamics study on the hydrogen abstraction reaction of oxygen atom with methylhydrazine

The mechanism of the multichannel reaction CH₃NHNH₂ (SC₁ and SC₂) + O → products is investigated theoretically using ab initio and density functional theory, and dynamics properties are explored by a dual‐level direct dynamics method. The calculation of the potential energy surface is carried out at the BMC‐CCSD//MPW1K/6‐311G(d,p) level. Using canonical variational transition state theory with a small‐curvature tunneling correction, the rate constants of each channel are evaluated over a wide temperature range of 200–2000 K on the basis of obtained electronic structures and energy information. The total rate constants are calculated from the sum of the individual rate constants taking into account the Boltzmann distribution of two conformers. The reactivity of the H atom located in different groups is compared. © 2013 Wiley Periodicals, Inc.     

Mechanistic insight on (E)‐methyl 3‐(2‐aminophenyl)acrylate cyclization reaction by multicatalysis of solvent and substrate

The reaction mechanism of (E)‐methyl 3‐(2‐aminophenyl)acrylate ( A ) with phenylisothiocyanate ( B ) as well as the vital roles of substrate A and solvent water were investigated under unassisted, water‐assisted, substrate A ‐assisted, and water‐ A ‐assisted conditions. The reaction proceeds with four processes via nucleophilic addition, deprotonation and protonation, intramolecular cyclization with hydrogen transfer, and keto–enol tautomerization. According to the different H‐shift mode, two possible types of H‐shift P1 and P2 are carefully investigated to identify the most preferred pathway, differing in the ? NH₂ group deprotonation and ? CH group of A protonation processes. It is found that substrate A and water not only act as reactant and solvent, but also as catalyst, proton shuttle, and stabilizer in effectively lowering the energy barrier. Therefore, the results demonstrate that the strong donating and accepting ability of ? NH₂ group on A and the presence of bulk water are the keys to the title reaction proceed. © 2016 Wiley Periodicals, Inc.     

Roles of K151 and D180 in L‐2‐haloacid dehalogenase from Pseudomonas sp. YL: Analysis by molecular dynamics and ab initio fragment molecular orbital calculations

L ‐2‐haloacid dehalogenase (L ‐DEX) catalyzes the hydrolytic dehalogenation of L ‐2‐haloalkanoic acids to produce the corresponding D ‐2‐hydroxyalkanoic acids. This enzyme is expected to be applicable to the bioremediation of environments contaminated with halogenated organic compounds. We analyzed the reaction mechanism of L ‐DEX from Pseudomonas sp. YL (L ‐DEX YL) by using molecular modeling. The complexes of wild‐type L ‐DEX YL and its K151A and D180A mutants with its typical substrate, L ‐2‐chloropropionate, were constructed by docking simulation. Subsequently, molecular dynamics (MD) and ab initio fragment molecular orbital (FMO) calculations of the complexes were performed. The ab initio FMO method was applied at the MP2/6‐31G level to estimate interfragment interaction energies. K151 and D180, which are experimentally shown to be important for enzyme activity, interact particularly strongly with L ‐2‐chloropropionate, catalytic water, nucleophile (D10), and with each other. Our calculations suggest that K151 stabilizes substrate orientation and balances the charge around the active site, while D180 stabilizes the rotation of the nucleophile D10, fixes catalytic water around D10, and prevents K151 from approaching D10. Further, D180 may activate catalytic water on its own or with K151, S175, and N177. These roles are consistent with the previous results. Thus, MD and ab initio FMO calculations are powerful tools for the elucidation of the mechanism of enzymatic reaction at the molecular level and can be applied to other catalytically important residues. The results obtained here will play an important role in elucidating the reaction mechanism and rational design of L ‐DEX YL with improved enzymatic activity or substrate specificity. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Reversible Adaptation to Photoinduced Shape Switching by Oligomer–Macrocycle Interconversion with Component Selection in a Three‐State Constitutional Dynamic System

Light irradiation of the molecular photoswitch 1 ‐E causes isomerization into the 1 ‐Z configuration stabilized by an internal hydrogen bond. 1 ‐E bears aldehyde groups allowing for dynamic covalent reaction with linear diamines. On photoinduced E/Z shape switching of 1 in presence of diamines, the system undergoes interconversion between two states, a non‐cyclic oligomeric one and a macrocyclic one, corresponding respectively to the E and Z configurations of 1 . With a mixture of linear α,ω‐diamines, 1 ‐E yields non‐selective dynamic oligomers by random incorporation of diamine components. Photoswitching to the 1 ‐Z form leads to constitutional adaptation with preferential formation of the macrocycle incorporating the best suited diamine, H₂N(CH₂)₇NH₂. In presence of metal cations, the E form switches from its unbound W shape to its coordinated U shape and yields the macrocycle resulting from the selective incorporation of the diamine H₂NCH₂CH₂OCH₂CH₂NH₂ that contains an additional O coordination site. Taken together, the results obtained describe constitutional adaptation in a triple state system: an oligomeric one and two different macrocyclic ones generated in response to two orthogonal agents, a physical stimulus, light, or a chemical effector, metal cations. These three states present, towards the incorporation of diamine components, respectively no selection, photoselection and metalloselection.     

Pentopyranosyl Oligonucleotide Systems,Communication No.12, The β‐D‐Xylopyranosyl‐(4′→2′‐oligonucleotide System

β‐D ‐Xylopyranosyl‐(4′→2′)‐oligonucleotides containing adenine and thymine as nucleobases were synthesized as a part of a systematic study of the pairing properties of pentopyranosyl oligonucleotides. Contrary to earlier expectations based on qualitative conformational criteria, β‐D ‐xylopyranosyl‐(4′→2′)‐oligonucleotides show Watson‐Crick pairing comparable in strength to that shown by pyranosyl‐RNA.     

Ab initio study of the high‐temperature phase transition in crystalline GeO2

Germanium dioxide (GeO₂) takes two forms at ambient pressure: a thermodynamically stable rutile‐type structure and a high‐temperature quartz‐type polymorph. Here, we investigate the phase stability at finite temperatures by ab initio phonon and thermochemical computations. We use gradient‐corrected density‐functional theory (PBE‐GGA) and pay particular attention to the modeling of the “semicore” germanium 3d orbitals (ascribing them either to the core or to the valence region). The phase transition is predicted correctly in both cases, and computed heat capacities and entropies are in excellent agreement with thermochemical database values. Nonetheless, the computed formation energies of α‐quartz‐type GeO₂ (and, consequently, the predicted transition temperatures) differ significantly depending on theoretical method. Remarkably, the simpler and cheaper computational approach produces seemingly better results, not worse. In our opinion, GeO₂ is a nice test case that illustrates both possibilities and limitations of modern ab initio thermochemistry. © 2013 Wiley Periodicals, Inc.