Theoretically modelling the water bilayer on the Al(111) surface using cluster calculations

Calvin, Mark D.; Head, John D.; Jin, Suqian

doi:10.1016/0039-6028(95)00862-4

Cited by 41 publications

(31 citation statements)

References 13 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To overcome these critical points, we have combined the HMR approach with the PHVA [31][32][33][34][35][36][37].…”

Section: Methodologiesmentioning

confidence: 99%

“…Similarly to a previous work of some of the present authors on amide vibrational couplings in small peptides [19], in this paper, we will apply a computational strategy still based on the PCM combined with the HMR method and Partial hessian vibrational approach (PHVA) [31][32][33][34][35][36][37] to evaluate interand intra-layer couplings between hydrogen bonded and stacked DNA base pairs. In particular, the coupling between carbonyl vibrations located on G and C bases will be considered in the case of a A-form DNA of well-known structure, resolved with X-ray crystallography [38].…”

Section: Introductionmentioning

confidence: 98%

See 1 more Smart Citation

Modelling vibrational coupling in DNA oligomers: a computational strategy combining QM and continuum solvation models

et al. 2012

View full text Add to dashboard Cite

In this paper, a computational strategy, based on DFT calculations at the M06-2X level, combined with the polarizable continuum model, the Hessian matrix reconstruction method and the Partial hessian vibrational approach is applied to evaluate inter-and intra-layer vibrational couplings between hydrogen bonded and stacked DNA base pairs. The present work demonstrates that this computational scheme can effectively predict and interpret the vibrational couplings of nucleic acids in solution. The effect of the environment described in a cluster or in a continuum manner is necessary in order to improve the agreement with the experimental values.

show abstract

“…To overcome these critical points, we have combined the HMR approach with the PHVA [31][32][33][34][35][36][37].…”

Section: Methodologiesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 98%

Modelling vibrational coupling in DNA oligomers: a computational strategy combining QM and continuum solvation models

et al. 2012

View full text Add to dashboard Cite

show abstract

“…Such a partial geometry optimization with fixed hydrogens asks for an adapted NMA method: the saturating hydrogens should also be kept fixed during the vibrational analysis to ensure consistency. This is accomplished by the Partial Hessian Vibrational Analysis (PHVA), where first the rows and columns corresponding to the fixed atoms are deleted from the Hessian and then this smaller submatrix is diagonalized [39,40,41,42,43]. This NMA scheme is labeled as PHVA H , referring to the hydrogens as the fixed atoms.…”

Section: Theoretical Simulationsmentioning

confidence: 99%

“…In the latter work, large finite clusters and a hybrid QM/MM ONIOM calculation scheme were applied. The large finite clusters were saturated with fixed outer hydrogens and a normal mode analysis was hence performed using the partial hessian vibrational analysis (PHVA) method [39,40,41,42,43]. In addition to the PHVA scheme, other vibrational analysis schemes can be applied to study extended systems.…”

Section: Introductionmentioning

confidence: 99%

Experimental and theoretical IR study of methanol and ethanol conversion over H-SAPO-34

Hemelsoet

Ghysels

et al. 2011

Catalysis Today

View full text Add to dashboard Cite

Theoretical and experimental IR data are combined to gain insight into the methanol and ethanol conversion over an acidic H-SAPO-34 catalyst. The theoretical simulations use a large finite cluster and the initial physisorption energy of both alcohols is calculated.Dispersive contributions turn out to be vital and the final adsorption of ethanol is predicted to be stronger compared to methanol (difference of 14 kJ mol −1 ). Calculated IR spectra of the alcohols and of formed aromatic cations upon conversion are also analyzed and support the peak assignment of the experimental in situ DRIFT spectra, in particular for the C-H and C=C regions. Theoretical IR spectra of the gas phase compounds are compared with those of the molecules loaded in a SAPO cluster and the observed shifts of the peak positions are discussed. To get a better understanding of these framework-guest interactions, a new theoretical procedure is proposed based on a normal mode analysis.A cumulative overlap function is defined and enables the characterization of individual peaks as well as induced frequency shifts upon adsorption.

show abstract

“…An example of such a partial optimization is the simulation of reactions at surfaces, where the reactive center's geometry is optimized but the rest of the sur-face is kept fixed during the optimization. 7 The computation of the frequencies in such partially optimized systems is far from trivial. The main problem is that the global system is in nonequilibrium, and application of the standard NMA procedure is wrong, leading to wrong frequencies, 8 which may even include a series of spurious imaginary frequencies.…”

Section: Introductionmentioning

confidence: 99%

Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach

Ghysels

Neck

Brooks

et al. 2009

The Journal of Chemical Physics

View full text Add to dashboard Cite

In a previous paper [Ghysels et al., J. Chem. Phys. 126, 224102 (2007)] the mobile block Hessian (MBH) approach was presented. The method was designed to accurately compute vibrational modes of partially optimized molecular structures. The key concept was the introduction of several blocks of atoms, which can move as rigid bodies with respect to a local, fully optimized subsystem. The choice of the blocks was restricted in the sense that none of them could be connected, and also linear blocks were not taken into consideration. In this paper an extended version of the MBH method is presented that is generally applicable and allows blocks to be adjoined by one or two common atoms. This extension to all possible block partitions of the molecule provides a structural flexibility varying from very rigid to extremely relaxed. The general MBH method is very well suited to study selected normal modes of large macromolecules (such as proteins and polymers) because the number of degrees of freedom can be greatly reduced while still keeping the essential motions of the molecular system. The reduction in the number of degrees of freedom due to the block linkages is imposed here directly using a constraint method, in contrast to restraint methods where stiff harmonic couplings are introduced to restrain the relative motion of the blocks. The computational cost of this constraint method is less than that of an implementation using a restraint method. This is illustrated for the alpha-helix conformation of an alanine-20-polypeptide.

show abstract

Theoretically modelling the water bilayer on the Al(111) surface using cluster calculations

Cited by 41 publications

References 13 publications

Modelling vibrational coupling in DNA oligomers: a computational strategy combining QM and continuum solvation models

Modelling vibrational coupling in DNA oligomers: a computational strategy combining QM and continuum solvation models

Experimental and theoretical IR study of methanol and ethanol conversion over H-SAPO-34

Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach

Contact Info

Product

Resources

About