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The characteristics of interaction between six transition-metal porphyrines and the Ag(111) surface are detailed here as resulted from DFT calculations. Van der Waals interactions as well as the strong correlation in 3d orbitals of transition metals were taken into account in all calculations, including the structural relaxation. For each system we investigate four relative positions of the metallic atom on top the surface. We show that the interaction between the transition metal and silver is the result of a combination between the dispersion interaction, charge transfer and weak chemical interaction. The detailed analysis of the physical properties, such as dipolar and magnetic moments and the molecule–surface charge transfer, analyzed for different geometric configurations allows us to propose qualitative models, relevant for the understanding of the self-assembly processes and related phenomena.

Using first-principles calculations, we investigate the binding energy for six transition metal - phthalocyanine molecules adsorbed on Au(111). We focus on the effect of translation on molecule - surface physical properties; van der Waals interactions as well as the strong correlation in d orbitals of transition metals are taken into account in all calculations. We found that dispersion interaction and charge transfer have the dominant role in the molecule-surface interaction, while the interaction between the transition metal and gold has a rather indirect influence over the physics of the molecule-surface system. A detailed analysis of the physical properties of the adsorbates at different geometric configurations allows us to propose qualitative models to account for all values of interface dipole charge transfer and magnetic moment of metal-phthalocyanines adsorbed on Au(111).

We present a theoretical investigation that addresses the most important aspects of the interaction between α-glycero-phosphatidyl-choline and Au(111) surface. For the density functional calculations we employed both traditional exchange-correlation functionals and newly developed vdW-D2 corrected one. The comparison between these functionals allows us to spot the role of van der Waals effects into the molecule– surface interaction. The effect of an external field applied to the molecule–surface system was also explicitly investigated. Our results reveal a complex picture where the molecular adsorption is dominated by the interplay between a weak molecule–surface interaction and a rather important deformation energy of the adsorbed molecule. In the presence of an external electric field, the choline moiety provided the strongest response in terms of binding energy as well as geometric configuration of the adsorbate.

We investigate the weak interactions taking place in the tetraphenylporphyrin dimers by using Wannier orbitals and DFT. The Van der Waals interaction energies for various geometric configurations of the dimers are then compared to the differences between the total DFT energies of dimers and those of sums over the energies of monomers. The comparison allows us to estimate the weight of the Van der Waals contribution to the total interaction energy since the DFT values include all contributions such as weak chemical interaction or Pauli repulsion to the binding energy. We show that the interaction energy computed with vdW-DF-cx exchange-correlation functional is almost identical with the one computed using Wannier orbitals. By analyzing the properties of Wannier orbitals in monomer and dimer structures, we check the fact the Van der Waals energy can be accurately calculated by using only the orbitals corresponding to the single molecule, which is useful from a practical perspective.

The molecular doping of graphene with π-stacked conjugated molecules has been widely studied during the last 10 years, both experimentally or using first-principle calculations, mainly with strongly acceptor or donor molecules. Macrocyclic metal complexes have been far less studied and their behavior on graphene is less clear-cut. The present density functional theory study of cobalt porphyrin and phthalocyanine adsorbed on monolayer or bilayer graphene allows to compare the outcomes of two models, either a finite-sized flake of graphene or an infinite 2D material using periodic calculations. The electronic structures yielded by both models are compared, with a focus on the density of states around the Fermi level. Apart from the crucial choice of calculation conditions, this investigation also shows that unlike strongly donating or accepting organic dopants, these macrocycles do not induce a significant doping of the graphene sheet and that a finite size model of graphene flake may be confidently used for most modeling purposes. © 2017 Wiley Periodicals, Inc.

In this work the surface-enhanced Raman total half band widths of seven genomic DNAs from leaves of chrysanthemum (Dendranthema grandiflora Ramat.), common sundew (Drosera rotundifolia L.), edelweiss (Leontopodium alpinum Cass), Epilobium hirsutum L., Hypericum richeri ssp. transsilvanicum (Čelak) Ciocârlan, rose (Rosa x hybrida L.) and redwood (Sequoia sempervirens D. Don. Endl.) have been measured. We have shown that surface-enhanced Raman spectroscopy (SERS) can be used to study the fast subpicosecond dynamics of DNA in the proximity of a metallic surface. The dependencies of the total half band widths and the global relaxation times, on the DNA molecular subgroup structure and on the type of genomic DNA, are reported. In our study, the full widths at half-maximum (FWHMs) for the SERS bands of genomic DNAs from different leaf tissues are typically in the wavenumber range from 15 to 55 cm(-1). Besides, it can be observed that molecular relaxation processes studied in this work have a global relaxation time smaller than 0.71 ps and larger than 0.19 ps. A comparison between different ranges of FT-Raman and SERS band parameters, respectively, corresponding to DNA extracted from leaf tissues is given. It is shown that the interaction between DNA and a metallic surface has the potential to lead to a shortening of the global relaxation times, as compared with molecular dynamics in solution. We have found that the surface dynamics of molecular subgroups in plant DNA is, in some cases, about two times faster than the solution dynamics of nucleic acids. This can be rationalized in a qualitative manner by invoking the complex landscape of the interaction energy between the molecule and the silver surface.

We examine the ballistic conduction through Au-NiMnSb-Au heterostructures consisting of up to four units of NiMnSb in the scattering region. We investigate the dependence of the transmission function computed within the local spin density approximation (LSDA) of the density functional theory (DFT) on the number of half-metallic units in the scattering region. For a single NiMnSb unit the transmission function displays a spin polarization of around 50 % in a window of 1 eV centered around the Fermi level. By increasing the number of layers an almost complete spin polarization of the transmission is obtained in the same energy window. Supplementing the DFT-LSDA calculations with local electronic interactions, of Hubbard-type on the Mn sites, leads to a hybridization between the interface and many-body states. The significant reduction of the spin polarization seen in the density of states is not apparent in the spin-polarization of the conduction electron transmission, which suggests the localized nature of the hybridized interface and many-body induced states., 25 pages, 6 figures

We present density functional theory investigations on the electronic structure properties for three derivatives of trioxotriangulene that were recently used as electrode materials in Li–ion batteries. We compare the results obtained by standard GGA exchange–correlation functionals with those based on recently developed van der Waals exchange–correlation functionals for the free molecules and bulk structures. This allows us to point out the importance of van der Waals interaction for the stability of the structures as well as the main characteristics of the electronic structures.

Surface enhanced Raman scattering (SERS) effect is currently exploited as the basis of a new type of optical labels for in vivo investigation of the tissues, especially for early medical diagnostic. Silver colloidal nanoparticles decorated with chemisorbed cresyl violet molecular species could act as hybrid SERS labels. Their Raman scattering properties have been characterized here using different SERS techniques, and probing different excitation wavelengths, even in the near infrared. Obtaining FT-SERS signal of cresyl violet is of particular importance for applying FT-Raman spectroscopy to the tissues or cells, in providing sensitive information in the close vicinity of the SERS label incubated into the biological sample. Furthermore, upon chemisorption on the silver nanoparticles, cresyl violet molecular orientation provided both amino functional groups free of interaction with the silver, resulting double amino-functionalized Ag nanoparticles suitable for DNA tagging. SERS tests of melanoma induced in mouse using CV-Ag SERS label suggested the possibility to setup the tissue labeling procedure for skin cancer monitoring.(doi: 10.5562/cca2067)

We investigate the vibrational properties of pentagonal and hexagonal single walled silicon nanotubes by using DFT and the frozen phonons method. The phononic band structure and the vibrational density of states are reported. The stability of each structure is discussed based on these results. We investigate the influence of isotopic substitutions upon the vibrational density of states for the two types of nanotubes. Finally, we show that the model of vibrational Hamiltonian in a diatomic chain can be used to give a qualitative description of the relation between the amount of isotopically substituted layers in the nanotube and their influence upon the vibrational density of states.

We have investigated the ballistic transport for Mn, Fe-porphyrin molecules in contact with Au(111) electrodes by using density functional theory. We show that the information resulted from the projected density of electronic states does not provide a complete picture of the transport mechanism. Instead, we propose a methodology based on the concept of the orbital projected transmissions for selected groups of atoms. We have found that the transmission channels for occupied states can be assigned to short range scattering processes at gold-molecule interface, while for the states above Fermi level the transmission takes place via long range scattering processes. The interplay between these two conduction mechanisms is responsible for the transport path in metal-porphyrin; our model is in qualitative agreement with the existing experimental data on transport pathway on single porphyrin molecules.

We propose a method to compute the transmission through correlated heterostructures by combining density functional and many-body dynamical mean field theories. The heart of this combination consists in porting the many-body self-energy from an all electron basis into a pseudopotential localized atomic basis set. Using this combination we study the effects of local electronic interactions and finite temperatures on the transmission across the ${\text{Cu}}_{4}\text{Co}{\text{Cu}}_{4}$ metallic heterostructure. It is shown that as the electronic correlations are taken into account via a local but dynamic self-energy, the total transmission at the Fermi level gets reduced (predominantly in the minority-spin channel), whereby the spin polarization of the transmission increases. The latter is due to a more significant $d$-electron contribution, as compared to the noncorrelated case in which the transport is dominated by $s$ and $p$ electrons.

Theoretical density functional theory (DFT) calculation, ab initio and experimental vibrational characterization of acridone were performed. The computed vibrational modes agree well with the experimental values of the related crystal structure. Surface enhanced Raman scattering (SERS) of acridone in silver colloids with different surface potential values was studied. FT-SERS spectrum of acridone revealed different adsorption behavior of the title compound on the silver particles.

We compare the density functional theory (DFT) results on the adsorption of small aromatic molecules (benzene, pyridine and thiophene) on gold surfaces obtained by using three types of van der Waals exchange-correlation functionals and localized basis set calculations. We show that the value of the molecule surface binding energy depends on the interplay between the BSSE effect and the tendency of the exchange-correlation functionals to overestimate both the molecule-surface as well as the gold-gold distances within the relaxed systems. Consequently, we find that by using different types of LCAO basis sets or geometric models for the adsorption of the molecules on the surface, the binding energy can vary up to 100 %. A critical analysis of the physical parameters resulting from the calculations is presented for each exchange-correlation functional.

Theoretical ab initio (3-STO) and semiempiric (PM3) IR spectra of isolated B 6 vitamin (pyridoxine hydrochloride) molecule have been obtained and found in good agreement with the experimental IR spectrum. FT-Raman spectrum of the B 6 vitamin in solid polycrystalline state, polarised Raman as well as the Raman and SERS spectra on Ag colloidal surface at different pH have been recorded and discussed. The protonated or deprotonated form of the B 6 molecule was evidenced from the pH dependence Raman spectra. SERS bands associated to the chemical interaction between the deprotonated N ring atom and Ag colloidal particles were absent. Compared to related polysubstituted pyridine molecules, a different SERS behaviour of B 6 molecule was concluded.

The geometrical properties and electronic structure of DNA nucleosides (deoxyadenosine, thymidine, deoxyguanosine, deoxycytidine) adsorbed on a metallic surface of Cu(111) are determined using density functional theory computations. In order to assess the effect of the long-range interaction upon the results of the DFT simulations, we compare the results of a standard GGA exchange-correlation functional with those produced by the newly developed van der Waals exchange-correlation functional. The most striking difference between the two sets of results occurs for the adsorption energies: standard functional predicts values representing about 30% of those obtained when van der Waals interaction is taken into account. The standard GGA functional favors slightly tilted orientation of the DNA bases with respect to the surface, while the inclusion of the van der Waals effect leads to an almost parallel orientation of the bases with the surface. On the other hand, the position of the sugar pucker is less influenced by the type of the exchange-correlation used. According to our studies, in the presence of long-range interactions, the molecule-surface charge transfer is qualitatively affected. Standard functional predicts a decrease of the electronic population of the adsorbate, while the presence of long-range interaction leads to an opposite effect.

Using first-principles calculations, we study the electronic properties of 1-4, dicyanobenzene and 1-4, phenylene diisocyanide molecules sandwiched between two Pt(111) and Pd(111) electrodes. For these metal-molecule-metal systems, we calculate the total and local density of states and the charge transfers. Our results suggest that the tunneling is the dominant mechanism of charge transport. By inducing a shift of the Fermi level of about 2 eV via an additional gate electrode, the electronic transmission could be significantly increased through the metal-1-4, phenylene diisocyanide-metal systems, but a higher voltage would be required in the metal-1-4, dicyanobenzene-metal devices.

Large changes in the Raman spectra of calf thymus DNA are observed uponlowering the pH. In order to gain a better insight into these effects, several simulationsof the Raman spectra of the guanine-cytosine (GC) Watson–Crick and Hoogsteen basepairs are performed. By comparing the Raman bands of GC base pairs in calf thymusDNA at high and low pH with the theoretical simulations of GC base pairs, it is foundthat the intensity changes in the theoretical bands located between 400 and 1000 cm 1 are small compared to the experimental ones. The behavior of the cytosine band at 1257cm 1 upon lowering the pH is not reproduced in the GC theoretical spectra. The bandslocated above 1300 cm 1 in the theoretical spectra display intensity changes that aresimilar to those found for GC base pairs in calf thymus DNA spectra. © 2003 WileyPeriodicals, Inc. Biopolymers (Biospectroscopy) 72: 339–344, 2003 Keywords: GC base pairs; Watson–Crick; Hoogsteen; Raman spectra; density func-tional theory calculations