Chlorophyll and pheophytin protonated and deprotonated ions: Observation and theory.

Pheophytin a and chlorophyll a have been investigated by electrospray mass spectrometry in the positive and negative modes, in view of the importance of the knowledge of their properties in photosynthesis. Pheophytin and chlorophyll are both observed intensely in the protonated mode, and their main fragmentation route is the loss of their phytyl chain. Pheophytin is observed intact in the negative mode, while under collisions, it is primarily cleaved beyond the phytyl chain and loses the attaching propionate group.

Insight into Substrate Recognition by Urea-Based Helical Foldamer Catalysts Using a DFT Global Optimization Approach.

Peptides and foldamers have recently gained increasing attention as chiral catalysts to achieve challenging (asymmetric) transformations. We previously reported that short helically folded aliphatic oligoureas in combination with achiral Brønsted bases are effective H-bonding catalysts for C-C bond-forming reactions─i.e.

Vibrational treatment of hydroxylamine in valence coordinates.

A valence coordinate HNOH ground state potential energy surface accurate for all levels up to 6000 cm relative to trans zero point energy has been generated at the coupled-cluster single double triple-F12/aug-cc-pVTZ level encompassing the trans and cis as well as the N-H permutational conformers. All cis and trans fundamentals and a complete set of eigenfunctions up to about 3100 cm have been calculated and assigned using the improved relaxation method of the Heidelberg multi-configuration time-dependent Hartree package and an exact expression for the kinetic energy in valence coordinates generated by the TANA program. The average and maximal error to all observed transitions is about 6.

The CRYSTAL code, 1976-2020 and beyond, a long story.

CRYSTAL is a periodic ab initio code that uses a Gaussian-type basis set to express crystalline orbitals (i.e., Bloch functions).

Calculation of Anharmonic IR and Raman Intensities for Periodic Systems from DFT Calculations: Implementation and Validation.

An extension of the CRYSTAL program is presented allowing for calculations of anharmonic infrared (IR) intensities and Raman activities for periodic systems. This work is a follow-up of two papers devoted to the computation of anharmonic vibrational states of solids from DFT (density functional theory) calculations (Erba et al. 2019, 15, 3755-3765 and Erba et al.

Vibrational states of deuterated trans- and cis-formic acid: DCOOH, HCOOD, and DCOOD.

The vibrational eigenenergies of the deuterated forms of formic acid (DCOOD, HCOOD, and DCOOH) have been computed using the block-improved relaxation method, as implemented in the Heidelberg multiconfiguration time-dependent Hartree package on a previously published potential energy surface [F. Richter and P. Carbonnière, J.

Anharmonic Vibrational States of Solids from DFT Calculations. Part II: Implementation of the VSCF and VCI Methods.

Two methods are implemented in the Crystal program for the calculation of anharmonic vibrational states of solids: the vibrational self-consistent field (VSCF) and the vibrational configuration-interaction (VCI). While the former is a mean-field approach, where each vibrational mode interacts with the average potential of the others, the latter allows for an explicit and complete account of mode-mode correlation. Both schemes are based on the representation of the adiabatic potential energy surface (PES) discussed in Part I, where the PES is expanded in a Taylor's series so as to include up to cubic and quartic terms.

Anharmonic Vibrational States of Solids from DFT Calculations. Part I: Description of the Potential Energy Surface.

A computational approach is presented to compute anharmonic vibrational states of solids from quantum-mechanical DFT calculations by taking into explicit account phonon-phonon couplings via the vibrational configuration interaction (VCI) method. The Born-Oppenheimer potential energy surface (PES) is expanded in a Taylor's series in terms of harmonic normal coordinates, centered at the equilibrium nuclear configuration, is truncated to quartic order, and contains one-mode, two-mode, and three-mode interatomic force constants. The description of the anharmonic terms of the PES involves the numerical evaluation of high-order energy derivatives (cubic and quartic in our case) with respect to nuclear displacements and constitutes the most computationally demanding step in the characterization of anharmonic vibrational states of materials.

Vibrational treatment of the formic acid double minimum case in valence coordinates.

One single full dimensional valence coordinate HCOOH ground state potential energy surface accurate for both cis and trans conformers for all levels up to 6000 cm relative to trans zero point energy has been generated at CCSD(T)-F12a/aug-cc-pVTZ level. The fundamentals and a set of eigenfunctions complete up to about 3120 and 2660 cm for trans- and cis-HCOOH, respectively, have been calculated and assigned using the improved relaxation method of the Heidelberg multi-configuration time-dependent Hartree package and an exact expression for the kinetic energy in valence coordinates generated by the TANA program. The calculated trans fundamental transition frequencies agree with experiment to within 5 cm.

The VNH defect in diamond: a quantum-mechanical characterization.

The VNH defect in diamond (a vacancy surrounded by three nitrogen and one carbon atoms, the latter being saturated by a hydrogen atom) is investigated quantum-mechanically by use of a periodic supercell approach, an all-electron Gaussian-type basis set, "hybrid" functionals of density functional theory, and the Crystal program. Three fully optimized structural models (supercells containing 32, 64, and 128 atoms) are considered to investigate the effect of defect concentration. The electronic configuration of the defect is reported along with a description of its structural features.

Vibrational Fingerprints of Low-Lying Pt(n)P(2n) (n = 1-5) Cluster Structures from Global Optimization Based on Density Functional Theory Potential Energy Surfaces.

Vibrational fingerprints of small Pt(n)P(2n) (n = 1-5) clusters were computed from their low-lying structures located from a global exploration of their DFT potential energy surfaces with the GSAM code. Five DFT methods were assessed from the CCSD(T) wavenumbers of PtP2 species and CCSD relative energies of Pt2P4 structures. The eight first Pt(n)P(2n) isomers found are reported.

Anharmonic Vibrational Treatment Exclusively in Curvilinear Valence Coordinates: The Case of Formamide.

A highly correlated approach using curvilinear valence coordinates is applied to calculate the vibrational fundamentals and some combination modes of the formamide molecule with high accuracy. A series of potential energy surfaces (PESs) has been generated by AGAPES, a program for adaptive generation of adiabatic PESs, at various electronic structure qualities until excellent nonaccidental agreement with the experimentally assigned fundamental transitions was reached at the CCSDT(T)-F12a/aug-cc-pVTZ level of theory using the improved relaxation method of the Heidelberg multiconfiguration time-dependent Hartree (MCTDH) package in connection with an exact expression for the kinetic energy in valence coordinates generated by the TANA program. By comparison of the overtone series ν1-3ν1 to experiment, we demonstrate that the known problems concerning the floppy ν1 wagging motion are solved within this approach.

Intramolecular vibrational redistribution in the non-radiative excited state decay of uracil in the gas phase: an ab initio molecular dynamics study.

We report a study of intramolecular vibrational distribution (IVR) occurring in the electronic ground state of uracil (S0) in the gas phase, following photoexcitation in the lowest energy bright excited state (Sπ) and decay through the ethylene-like Sπ/S0 Conical Intersection (CI-0π). To this aim we have performed 20 independent ab initio molecular dynamics simulations starting from CI-0π (ten of them with 1 eV kinetic energy randomly distributed over the different molecular degrees of freedom) and 10 starting from the ground state minimum (Franck-Condon, FC, point), with the excess kinetic energy equal to the energy gap between CI-0π and the FC point. The simulations, exploiting PBE0/6-31G(d) calculations, were performed over an overall period of 10 ps.

Piezoelectric, elastic, structural and dielectric properties of the Si(1-x)Ge(x)O(2) solid solution: a theoretical study.

We apply first principles quantum mechanical techniques to the study of the solid solution Si1-xGexO2 of α-quartz where silicon atoms are progressively substituted with germanium atoms, to different extents, as a function of the substitutional fraction x. For the first time, the whole range of the substitution (x = 0.0, 0.

Structural investigation of microhydrated thymine clusters and vibrational study of isolated and aqueous forms of thymine using DFT level of theory.

This theoretical study provides the physically reasonable structures of the microhydrated thymine clusters, from the mono- to the penta-hydrated species, by the exploration of their B3LYP and B3LYP-D potential energy surfaces using a global search algorithm of minima (GSAM). The anharmonic vibrational computations of the isolated and aqueous thymine are also reported. They were performed from B3LYP and B3LYP-D potential electronic surfaces followed by a second order perturbative treatment of the anharmonicity.

The electronic structure of MgO nanotubes. An ab initio quantum mechanical investigation.

The structural, vibrational and response properties of the (n,0) and (m,m) MgO nanotubes are computed by using a Gaussian type basis set, a hybrid functional (B3LYP) and the CRYSTAL09 code. Tubes in the range 6 ≤ n ≤ 140 and 3 ≤ m ≤ 70 were considered, being n = 2 × m the number of MgO units in the unit cell (so, the maximum number of atoms is 280). Tubes are built by rolling up the fully relaxed 2-D conventional cell (2 MgO units, with oxygen atoms protruding from the Mg plane alternately up and down by 0.

The use of the GSAM approach for the structural investigation of low-lying isomers of molecular clusters from density-functional-theory-based potential energy surfaces: the structures of microhydrated nucleic acid bases.

This study presents structural properties of microhydrated nucleic acid bases (NABs) - uracil (U), thymine (T), guanine (G), adenine (A), and cytosine (C) - investigated by theoretical computations at the B3LYP level of theory. To obtain the different representations of these microhydrated species, we applied the GSAM procedure: the most stable conformers labeled X,nH2O (X = U, T, G, A and n = 1..

Theoretical strategy to build structural models of microhydrated inorganic systems for the knowledge of their vibrational properties: the case of the hydrated nitrate aerosols.

This study provides theoretical anharmonic calculations for microhydrated NaNO3-labeled (NaNO3, nH2O)x with a water-to-solute ratio (n) ranging from 1 to 3. A representative geometrical model of these forms was first investigated by simulating the molecular clusters as (NaNO3,1H2O)x with x = 1 to 4. The comparison between the calculated time independent anharmonic frequencies using the B3LYP-D/6-311+G(d,p) method and their experimental counterparts led to the choice of a supercluster model.

An adaptive potential energy surface generation method using curvilinear valence coordinates.

An automatic Born-Oppenheimer potential energy surface (PES) generation method AGAPES is presented designed for the calculation of vibrational spectra of large rigid and semi-rigid polyatomic molecules within the mid-infrared energy range. An adaptive approach guided by information from intermediate vibrational calculations in connection with a multi-mode expansion of the PES in internal valence coordinates is used and its versatility is tested for a selection of molecules: HNO, HClCO, and formaldoxime. Significant computational savings are reported.

Doping-enhanced hyperpolarizabilities of silicon clusters: a global ab initio and density functional theory study of Si10 (Li, Na, K)n (n=1, 2) clusters.

A global theoretical study of the (hyper)polarizabilities of alkali doped Si(10) is presented and discussed. First, a detailed picture about the low lying isomers of Si(10)Li, Si(10)Na, Si(10)K, Si(10)Li(2), Si(10)Na(2), and Si(10)K(2) has been obtained in a global manner. Then, the microscopic first (hyper)polarizabilities of the most stable configurations have been determined by means of ab initio methods of high predictive capability such as those based on the Møller-Plesset perturbation and coupled cluster theory, paying extra attention to the (hyper)polarizabilities of the open shell mono-doped systems Si(10)Li, Si(10)Na, Si(10)K, and the influence of spin contamination.

Synthesis and characterization of NaBD3H, a potential structural probe for hydrogen storage materials.

Specifically labeled NaBD(3)H has been synthesized and characterized using X-ray diffraction, NMR, and vibrational spectroscopy. The isotopic purity of the compound, as estimated from NMR spectra, was found to be about 85% with the compound NaBD(2)H(2) as the second product. IR spectra confirm the relatively strong intensity of the single B-H stretching mode predicted from DFT calculations.

A global search algorithm of minima exploration for the investigation of low lying isomers of clusters from density functional theory-based potential energy surfaces: The example of Si(n) (n=3,15) as a test case.

Using an effective generation algorithm coupled with a PBE0/LANL2DZdp level of theory, 905 stable structures of Si(n) (n=3,15) have been found. This global search algorithm of minima exploration includes two original parts: the spheroidal generation, allowing the generation of rings, sphericals, m rings cylinders, and planar structures, and the raking optimization, which discards step by step the conformations that become physically unreasonable during the optimization process. The 142 isomers lying below 1 eV are reported and include the 28 structures reported in the literature.

Vibrational analysis of glycine radical: a comparative ab initio static and dynamic study.

We present quantum mechanical (QM) vibrational computations beyond the harmonic approximation for an organic molecule that exhibits both torsional and NH(2) out of plane type modes: the glycine radical. The effective second order perturbative, variational and variation-perturbation treatments-defined as static approaches-as well as vibrational analysis from ab initio molecular dynamics trajectories at 300 K and 600 K were performed using the B3LYP/6-31+G(d,p) description of the electronic structure. Theses schemes are compared in terms of prediction of fundamental transitions, simulation of the corresponding medium infrared (MIR) spectrum and extraction of substantial information for the understanding of chemical problems.

Fermi resonances of borohydrides in a crystalline environment of alkali metals.

Vibrational spectra of BH(4)(-) and its isotopic analogues in a crystalline environment of alkali metals cations (K(+), Rb(+), Cs(+)) have been investigated beyond the harmonic approximation using a variational approach supported by computations of B3LYP type anharmonic force fields. From the comparison of the observed and simulated IR spectra, the influence of the anharmonic couplings on the band position and on the relative intensity of the allowed vibrational transitions is discussed. Here, the effect of the crystalline environment induces a blue shift of about 50 and 100 cm(-1) respectively for the bending and stretching modes of BH(4)(-).

Calculations of vibrational energy levels by using a hybrid ab initio and DFT quartic force field: application to acetonitrile.

A hybrid quartic force field with quadratic force constants calculated at the CCSD(T)/cc-pVTZ level and cubic and quartic terms determined by a B3LYP/cc-pVTZ treatment is proposed to compute the vibrational energy levels of acetonitrile from a variational method. Fundamentals and overtones calculated in the range of 300-3200 cm(-1) are in fair agreement with the 31 observed data, with an absolute mean deviation of less than 0.8%.