Hydrogen-Bonding Networks from First-Principles: Exploring the Guanidine Crystal

Hoepfner, Veronika; Deringer, Volker L.; Dronskowski, Richard

doi:10.1021/jp2106132

Cited by 33 publications

(45 citation statements)

References 54 publications

(70 reference statements)

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“…The separation of charges, besides being favorable from the point of view of the balance between Coulomb interaction and demixing entropy, gains Lennard–Jones energy between Gnd ions (see Fig. S8 in the Supporting Information), presumably associated with hydrogen bonding between Gnd groups . The result is a minimum in the free energy of the system when the dipole associated with the helix assumes minimum modulus [cf., Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The effect of urea and GndCl on the states of fragment [22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38] Five simulations of the fragment 22-38, corresponding to the helix of GB1, were carried out in water, 2M urea, 5M urea, 2M GndCl and 4M GndCl, respectively, until convergence (cf., Figs. S1-S2 in the Supporting Information).…”

Section: Resultsmentioning

confidence: 99%

“…Experimental observables associated with fragment [22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38] From the ensemble of conformations generated by the simulation, one can calculate some macroscopic observables and compare them with those measured in experiments. Moreover, one can use these data to evaluate if their interpretation according to the standard view is compatible with the underlying conformational properties of the peptide, given by the model calculations.…”

Section: Figurementioning

confidence: 99%

“…Distribution of the solvent around fragment [22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38] The distribution of solvent around the peptide was investigated inspecting the radial distribution functions (rdf) of water and of denaturant molecules as a function of their minimum distance from any atom of each amino acid of the peptide. Two typical behaviors were found and illustrated in Figure 5, where the rdf associated with ALA26 and GLU27 are displayed (those associated with the other amino acids are displayed in Fig.…”

Section: Two-state Approximation and M Valuesmentioning

confidence: 99%

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Thermodynamic and structural effect of urea and guanidine chloride on the helical and on a hairpin fragment of GB1 from molecular simulations

Meloni

Tiana

2017

Proteins

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With the help of molecular-dynamics simulations, we studied the effect of urea and guanidine chloride on the thermodynamic and structural properties of the helical fragment of protein GB1, comparing them with those of its second beta hairpin. We showed that the helical fragment in different solvents populates an ensemble of states that is more complex than that of the hairpin, and thus the associated experimental observables (circular-dichroism spectra, secondary chemical shifts, m values), that we back-calculated from the simulations and compared with the actual data, are more difficult to interpret. We observed that in the case of both peptides, urea binds tightly to their backbone, while guanidine exerts its denaturing effect in a more subtle way, strongly affecting the electrostatic properties of the solution. This difference can have consequences in the way denaturation experiments are interpreted. Proteins 2017; 85:753-763. © 2016 Wiley Periodicals, Inc.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Figurementioning

confidence: 99%

Section: Two-state Approximation and M Valuesmentioning

confidence: 99%

See 2 more Smart Citations

Thermodynamic and structural effect of urea and guanidine chloride on the helical and on a hairpin fragment of GB1 from molecular simulations

Meloni

Tiana

2017

Proteins

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“…. N contacts, only those from amine to imine groups should be considered to be hydrogen-bonded [40].…”

Section: Refinement and Crystalmentioning

confidence: 99%

Synthesis, Crystal Structure, Polymorphism, and Magnetism of Eu(CN3H4)2 and First Evidence of EuC(NH)3

et al. 2017

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Abstract:We report the first magnetically coupled guanidinate, α-Eu(CN 3 H 4 ) 2 (monoclinic, P2 1 , a = 5.8494(3) Å, b = 14.0007(8) Å, c = 8.4887(4) Å, β = 91.075(6) • , V = 695.07(6) Å 3 , Z = 4). Its synthesis, polymorphism, crystal structure, and properties are complemented and supported by density-functional theory (DFT) calculations. The α-, β-and γ-polymorphs of Eu(CN 3 H 4 ) 2 differ in powder XRD, while the γ-phase transforms into the β-form over time. In α-Eu(CN 3 H 4 ) 2 , Eu is octahedrally coordinated and sits in one-dimensional chains; the guanidinate anions show a hydrogen-bonding network. The different guanidinate anions are theoretically predicted to adopt syn-, anti-and all-trans-conformations. Magnetic measurements evidence ferromagnetic interactions, presumably along the Eu chains. Finally, EuC(NH) 3 (isostructural to SrC(NH) 3 and YbC(NH) 3 , hexagonal, P6 3 /m, a = 5.1634(7) Å, c = 7.1993(9) Å, V = 166.23(4) Å 3 , Z = 2) is introduced as a possible ferromagnet.

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Analytic projection from plane-wave and PAW wavefunctions and application to chemical-bonding analysis in solids

et al. 2013

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Quantum-chemical computations of solids benefit enormously from numerically efficient plane-wave (PW) basis sets, and together with the projector augmented-wave (PAW) method, the latter have risen to one of the predominant standards in computational solid-state sciences. Despite their advantages, plane waves lack local information, which makes the interpretation of local densities-of-states (DOS) difficult and precludes the direct use of atom-resolved chemical bonding indicators such as the crystal orbital overlap population (COOP) and the crystal orbital Hamilton population (COHP) techniques. Recently, a number of methods have been proposed to overcome this fundamental issue, built around the concept of basis-set projection onto a local auxiliary basis. In this work, we propose a novel computational technique toward this goal by transferring the PW/PAW wavefunctions to a properly chosen local basis using analytically derived expressions. In particular, we describe a general approach to project both PW and PAW eigenstates onto given custom orbitals, which we then exemplify at the hand of contracted multiple-ζ Slater-type orbitals. The validity of the method presented here is illustrated by applications to chemical textbook examples-diamond, gallium arsenide, the transition-metal titanium-as well as nanoscale allotropes of carbon: a nanotube and the C60 fullerene. Remarkably, the analytical approach not only recovers the total and projected electronic DOS with a high degree of confidence, but it also yields a realistic chemical-bonding picture in the framework of the projected COHP method.

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Hydrogen-Bonding Networks from First-Principles: Exploring the Guanidine Crystal

Cited by 33 publications

References 54 publications

Thermodynamic and structural effect of urea and guanidine chloride on the helical and on a hairpin fragment of GB1 from molecular simulations

Thermodynamic and structural effect of urea and guanidine chloride on the helical and on a hairpin fragment of GB1 from molecular simulations

Synthesis, Crystal Structure, Polymorphism, and Magnetism of Eu(CN3H4)2 and First Evidence of EuC(NH)3

Analytic projection from plane-wave and PAW wavefunctions and application to chemical-bonding analysis in solids

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