Evaporatively cooled M+ (H2O)Ar cluster ions: infrared spectroscopy and internal energy simulations

Rotationally resolved IR spectra of M+ (H2O)Ar cluster ions for M=Na, K, and Cs in the O-H stretch region were measured in a triple-quadrupole mass spectrometer. Analysis of the spectra yields O-H stretch vibrational band origins and relative IR intensities of the symmetric and asymmetric modes. The effect of the alkali-metal ions on these modes results in frequency shifts and intensity changes from the gas phase values of water. The A-rotational constants are also obtained from the rotational structure and are discussed. Experimentally, the temperatures of these species were deduced from the relative populations of the K-rotational states. The internal energies and temperatures of the cluster ions for Na and K were simulated using RRKM calculations and the evaporative ensemble formalism. With binding energies and vibrational frequencies obtained from ab initio calculations, the average predicted temperatures are qualitatively consistent with the experimental values and demonstrate the additional cooling resulting from argon evaporation.     

Efficient and reliable calculation of rice-ramsperger—kassel-marcus unimolecular reaction rate constants for biopolymers: Modification of beyer-swinehart algorithm for degenerate vibrations

The Beyer-Swinehart (BS) algorithm, which calculates vibrational state density and sum, was modified for simultaneous treatment of degenerate vibrations. The modified algorithm was used in the grouped-frequency mode of the Rice-Ramsperger-Kassel-Marcus (RRKM) unimolecular reaction rate constant calculation for proteins with relative molecular mass as large as 100,000. Compared to the original BS method, reduction in computation time by a factor of around 3000 was achieved. Even though large systematic errors arising from frequency grouping were observed for state densities and sums, they more or less canceled each other, thus enabling reliable rate constant calculation. The present method is thought to be adequate for efficient and reliable RRKM calculations for any macromolecule in the gas phase such as the molecular ions of proteins, nucleic acids, and carbohydrates generated inside a mass spectrometer. The algorithm can also be used to calculate the internal energy distribution of a macromolecule at thermal equilibrium.     

Modeling carbon nanostructures with the self-consistent charge density-functional tight-binding method: vibrational spectra and electronic structure of C(28), C(60), and C(70)

The self-consistent charge density-functional tight-binding (SCC-DFTB) method is employed for studying various molecular properties of small fullerenes: C(28), C(60), and C(70). The computed bond distances, vibrational infrared and Raman spectra, vibrational densities of states, and electronic densities of states are compared with experiment (where available) and density-functional theory (DFT) calculations using various basis sets. The presented DFT benchmark calculations using the correlation-consistent polarized valence triple zeta basis set are at present the most extensive calculations on harmonic frequencies of these species. Possible limitations of the SCC-DFTB method for the prediction of molecular vibrational and optical properties are discussed. The presented results suggest that SCC-DFTB is a computationally feasible and reliable method for predicting vibrational and electronic properties of such carbon nanostructures comparable in accuracy with small to medium size basis set DFT calculations at the computational cost of standard semiempirical methods.     

Improved Whitten-Rabinovitch approximation for the Rice-Ramsperger-Kassel-Marcus calculation of unimolecular reaction rate constants for proteins

The Whitten-Rabinovitch (WR) approximation used in the semi-classical calculation of the Rice-Ramsperger-Kassel-Marcus (RRKM) unimolecular reaction rate constant was improved for reliable application to protein reactions. The state sum data for the 10-mer of each amino acid calculated by the accurate Beyer-Swinehart (BS) algorithm were used to obtain the residue-specific correction functions (w). The correction functions were obtained down to a much lower internal energy range than reported in the original work, and the cubic, rather than quadratic, polynomial was used for data fitting. For a specified sequence of amino acid residues in a protein, an average was made over these functions to obtain the sequence-specific correction function to be used in the rate constant calculation. Reliability of the improved method was tested for dissociation of various peptides and proteins. Even at low internal energies corresponding to the RRKM rate constant as small as 0.1 s-1, the rate constant calculated by the present method differed from the accurate BS result by 60% only. In contrast, the result from the original WR calculation differed from the accurate result by a factor of 3000. Compared to the BS method, which is difficult to use for proteins, the main advantage of the present method is that the RRKM rate constant can be calculated instantly regardless of the protein mass.     

Ab initio modeling of amide I coupling in antiparallel beta-sheets and the effect of 13C isotopic labeling on infrared spectra

Isotopic substitution with 13C on the amide C=O has become an important means of determining localized structural information about peptide conformations with vibrational spectroscopy. Various approaches to the modeling of the interactions between labeled amide sites, specifically for antiparallel two-stranded, beta-forming peptides, were investigated, including different force fields [dipole-dipole interaction vs density functional theory (DFT) treatments], basis sets, and sizes of model peptides used for ab initio calculations, as well as employing models of solvation. For these beta-sheet systems the effect of the relative positions of the 13C isotopic labels in each strand on their infrared spectra was investigated. The results suggest that the interaction between labeled amide groups in different strands can be used as an indicator of local beta-structure formation, because coupling between close-lying C=O groups on opposing chains leads to the largest frequency shifts, yet some alternate placements can lead to intensity enhancements. The basic character of the coupling interaction between labeled modes on opposing strands is independent of changes in peptide length, water solvent environment, twisting of the sheet structure, and basis set used in the calculations, although the absolute frequencies and detailed coupling magnitudes change under each of these perturbations. In particular, two strands of three amides each contain the basic interactions needed to simulate larger sheets, with the only exception that the C=O groups forming H-bonded rings at the termini can yield different coupling values than central ones of the same structure. Spectral frequencies and intensities were modeled ab initio by DFT primarily at the BPW91/6-31G** level for pairs of three, four, and six amide strands. Comparison to predictions of a classical coupled oscillator model show qualitative but not quantitative agreement with these DFT results.     

水分子配位对叶绿素a氧化还原势与红外光谱的影响

以光系统I反应中心电子传递链上的辅助叶绿素a为目标,采用密度泛函理论中的B3LYP方法,结合三种基组,系统计算了该叶绿素及其两种配位分子模型在气相、模拟蛋白质环境和水中的氧化还原势和离解能;同时计算了这三种模型在气相中的几何结构、红外光谱及其13C、15N和2H的同位素标记谱.计算及分析结果表明:水分子配位引起镁离子偏离叶绿素a的卟啉环平面中央,导致以镁原子为中心的键角减小,Mg—N键长增长;而天冬酰胺对配位的水分子施加氢键影响后,使得Mg—N键进一步增长,镁离子与水分子中氧原子的配位键Mg—O键长减小,离解能增加,合成分子的氧化还原势减少;另外,分子的氧化还原势和配位键离解能随着相对介电常数的增加以及计算基组的增大而减小;三种分子模型的羰基(C襒O)和卟啉环上C襒C键的特征振动频率差值小于7cm-1,而同位素标记引起其峰位变化量的差值小于3cm-1.该计算为研究光合反应中心电子传递链上叶绿素a的作用与功能提供理论参考依据.     

[M(Im)2X2]型配合物的Far-IR和Raman光谱的理论研究

本文用从头计算RHF和密度泛函B3LYP方法以及LanL2DZ，SDD和6-31G(d)基组计算了配合物M(Im)₂X₂ (Im=imidazole；M=Zn(Ⅱ)，Pd(Ⅱ)，Pt(Ⅱ)；X=F，Cl，Br，I)的几何构型以及Far-IR和Raman振动频率。计算结果表明，对Zn(Ⅱ)配合物而言,B3LYP/6-31G(d)方法得到的几何参数与实验值吻合得最好，B3LYP/SDD次之。在计算Far-IR和Raman振动频率时，发现采用6-31G(d)基组，两种方法计算的结果差别不大。对LanL2DZ和SDD基组而言，对计算结果影响较大的是理论方法，基组影响甚微，个别的振动频率基组影响较大，相比较而言，SDD基组得到的结果更好一些。本文所使用的两种计算方法都能得到与实验值比较吻合的结果，而用从头计算RHF方法计算的结果与实验值更接近一些。在此基础上，预测了Pd(Ⅱ)和Pt(Ⅱ)配合物的Far-IR和Raman振动频率。     

Benchmarking computational chemistry approaches on iminodiacetic acid

In the present study, theoretical harmonic vibrational frequencies (IR and Raman), carbon and proton NMR chemical shifts, geometric parameters, atomic charges (only for heteroatoms), reactivity indices (eLUMO, eHOMO, electronegativity, and hardness), and thermodynamical data (inner energy, enthalpy, Gibbs free energy, and entropy) of iminodiacetic acid (IDA) molecule have been investigated. We utilized ORCA software for B3LYP and HF (combined with Pople and Karlsruhe basis sets) calculations and MOPAC2016 software for semi-empirical calculations (AM1, PM3, and PM6). Theoretical vibrational frequencies and carbon and proton NMR chemical shifts have been compared with the corresponding experimental data. Although there was a strong correlation between the experimental and computational vibrational frequencies at low frequencies (<2200 cm^?1), the computational predictions of vibrational frequencies were unsuccessful at high frequencies (>2200 cm^?1). Distinctly, the studied computational approaches appeared to perform better in the prediction of carbon and proton NMR chemical shifts. Theoretical vibrational frequencies were also compared to each other to understand the impact of method choice (HF vs B3LYP D3 vs semi-empirical methods), dispersion correction (B3LYP D3 vs B3LYP), water solvation (SMD supplemented vs non-supplemented calculations), the family of basis set (Pople vs Karlsruhe basis sets), numbers of zeta (double vs triple zeta), polarization function (polarized vs nonpolarized basis sets), and diffusion function (diffusion supplemented vs non-supplemented basis sets). Moreover, geometric parameters, heteroatom charges, reactivity indices, and thermodynamical data produced by distinct computational approaches, as well, were compared to each other. Based on these comparisons, we detected critical factors (such as water solvation) acting on the computation of geometries, energies, and charges.     

Impact of local and density fitting approximations on harmonic vibrational frequencies

Harmonic vibrational frequencies are computed using second-order M?ller-Plesset perturbation theory (MP2) with and without local (LMP2) and density fitting (DF) approximations. Results for a test set of 17 small and medium size molecules (366 normal modes) are presented, and frequency scaling factors for LMP2 in combination with two different basis sets are determined. Comparison of the MP2 and LMP2 frequencies with experimental data reveals that the introduction of local approximations leads to a slightly better agreement with experiment. This is attributed to the reduction of basis set superposition errors in local calculations. Introduction of DF approximations within the LMP2 formalism leads to negligible deviations but significantly reduces the computational cost. These facts extend the applicability of the method to larger systems with large basis sets. As an example, the method is applied to a full DF-LMP2/cc-pVTZ frequency calculation for testosterone (49 atoms).     

A combined theoretical and experimental approach to the unimolecular loss of molecular hydrogen from protonated formaldehyde: Determination of the average internal energy of metastable [CH2OH]+ ions

Ab initio quantum chemical calculations (MP2/4–31G**) were performed for the dihydrogen elimination reaction from protonated formaldehyde. The energy difference between reactants and products and the activation energies were found to be in good agreement with the corresponding experimental quantities. Theoretical rate vs. energy curves were computed for a series of isotopic variants of the reaction using the Rice–Ramsperger–Kassel–Marcus (RRKM) method. The vibrational frequencies used in these calculations were taken from the 4–31G** geometry-optimized transition state and reactant structures. Quantum mechanical tunnelling was introduced to explain the existence of metastable CH₂OH ions, and a negative kinetic shift of about 0.1 eV was found. The intramolecular kinetic isotope effect for loss of HH/HD and DH/DD was calculated and compared with the experimental data. The result is consistent with the assumption that the average internal energy of metastable [CH₂OH]⁺ ions is very close to the critical energy for H₂ loss.     

Acetamide, a challenge to theory and experiment? On the molecular structure, conformation, potential to internal rotation of the methyl group and force fields of free acetamide as studied by quantum chemical calculations

The molecular geometry has been optimized without any constraints using different basis sets and levels of theory as: Hartree-Fock with basis sets 6–31+G**, 6–311++G**, cc-pVTZ and aug-cc-pVTZ, MP2 with basis sets 6–311++G** and cc-pVTZ, MP3 with basis set 6–311++G**, and density functional theory with basis sets 6–311++G** and cc-pVTZ. Small basis sets up to 6-31G predict the syn conformation of the methyl group to be the most stable conformation. Larger basis sets predict an unsymmetrical conformation with one of the H atoms perpendicular to the amide skeleton or an anti-like conformation. Dunnings correlation consistent polarized valence triple zeta, cc-pVTZ, basis set including MP2 predict two conformations, one perpendicular and one anti to be the most stable. The DFT calculations predict anti-like conformations. The most accurate calculations predict anti-like conformations which have not been predicted previously. The vibrational frequencies have been calculated for several basis sets and compared to the observed frequencies. The wagging frequency of the NH₂ is very dependent on the basis sets and levels of theory. Most calculations predict a planar NH₂ group in agreement with experiment. A scaled molecular force field has been determined by fitting the calculated frequencies to the observed ones for the perpendicular conformation using MP2/cc-pVTZ. The barrier heights for the methyl group have been calculated. The rotational constants, I_A + I_B − I_C values and dipole moments are compared with experimental values.     

Molecular density of states from estimated vapor phase heat capacities

Heat capacity data between 298 and 1500K are used to derive a reduced set of apparent vibrational frequencies that can be used for estimation of molecular density of states, ρ(E). Estimates for a number of molecule and radical species, using a reduced set of three frequencies with noninteger degeneracies, are shown to compare favorably to direct count methods, which require specification of the complete frequency set. Use of the reduced set of three frequencies leads to significant improvement in calculations of ρ(E)/Q as compared to similar calculations which use only a single geometric- or arithmetic-mean frequency approximation. Since vapor phase heat capacity data of molecules and radicals can be estimated accurately by a group additivity formalism, this approach provides a method to estimate ρ(E) for use in calculations of pressure effects in unimolecular and chemical activation reaction systems. The accuracy of the ρ(E)/Q distributions obtained from heat capacity data makes this a viable method for those cases where the complete frequency distribution is not known. It is especially valuable for those cases where contributions to ρ(E) from internal rotors or low frequency vibrations such as inversions are not well known. This approach is useful for quantum RRK or inverse Laplace transform calculations of k(E) since no assignment of transition state properties is necessary. The reduced frequency set can also be combined with ΔH_f(298) and S(298) to provide a compact data set to describe thermodynamic properties at any temperature. © 1997 John Wiley & Sons, Inc.     

Ab initio and DFT studies of the vibrational spectra of benzofuran and some of its derivatives

The vibrational spectra of benzofuran and some of its derivatives have been systematically investigated by ab initio and density functional B3LYP methods. The harmonic vibrational wavenumbers and intensity of vibrational bands were calculated at ab initio and DFT levels invoking different basis sets up to 6-311++g**. Vibrational assignments have been made and it has been found that the calculated DFT frequencies agree well in most cases with the observed frequencies for each molecule. Conformational studies have also been carried out and it is evident from ab initio calculations that 2(3H) benzofuranone is more stable than 3(2H) benzofuranone in support to our earlier semiempirical results.     

Theoretical studies on vibrational spectra of some halides of Group IIB elements

The vibrational spectra of Group IIB elements halides MX2 and their dimers M2X4 (M=Zn(II), Cd(II) and Hg(II); X=F, Cl, Br and I) have been systematically investigated by ab initio RHF and B3LYP methods with LanL2MB, LanL2DZ and SDD basis sets. The optimized geometries, calculated vibrational frequencies are evaluated via comparison with the experimental data. The vibrational frequencies, calculated by these methods with different basis sets, are compared to each other too. The best results can be obtained by RHF/SDD method, with this method, the deviations for MX2 and Hg2X4 are <7%. Some vibrational frequencies of M2X4 that have not been experimentally reported are also predicted.     

Structural and spectroscopic study of the van der Waals complex of CO with HCO+ and the isoelectronic complex of CS with HCS+

This work reports the results of high level ab initio calculations of the OC-HCO(+) complex and the SC-HCS(+) complex and their hydrogen migration transition states. Geometry optimizations are performed at the CCSD(T)/aug-cc-pV5Z level of theory. Subsequent frequency calculations are carried out at the CCSD(T)/aug-cc-pVQZ level of theory. Additional geometry optimizations and harmonic frequency calculations for all the species involved in this study have been done with the explicitly correlated CCSD(T)-F12 method with the aug-cc-pVTZ and VTZ-F12 basis set. The geometries, rotational constants, harmonic vibrational frequencies, and energetics of the species involved in the complex are reported. These methods result in accurate computational predictions that have mean deviations for bond lengths, rotational constants, and vibrational frequencies of 0.001 A?, 163 MHz, and 46 cm(-1), respectively. These results provide essential spectroscopic properties for the complexes that can facilitate both laboratory and interstellar observations, and they also provide a comparison between oxygen and sulfur complex observability based on thermodynamic stability.     

Anchoring the potential energy surface of the cyclic water trimer

Six cyclic stationary points on the water trimer potential energy surface have been fully optimized at the MP2 level with the aug-cc-pVQZ basis set. In agreement with previous work, harmonic vibrational frequencies indicate that two structures are minima, three are transition states connecting minima on the surface while the remaining stationary point is a higher-order saddle point. The 1- and n-particle limits of the electronic energies of each of these six structures were estimated by systematically varying both the basis sets and theoretical methods. The former limit was approached with the cc-pVXZ and aug-cc-pVXZ families of basis sets (X=2-7) while MP2, CCSD(T), and BD(TQ) calculations helped examine the latter. Core correlation effects have also been assessed at the MP2 level with the cc-pCVXZ series of basis sets (X=2-5). These data have been combined to provide highly accurate relative energies and dissociation energies for these stationary points.     

A computer program (COMPOST) for predicting mass spectrometric information from known amino acid sequences

A computer program (COMPOST) is described that carries out predictive computations on known amino acid sequences. The program is designed to be of use to mass spectrometrists with an interest in protein and peptide sequencing. Mass values (monoisotopic and average) for protonated peptide and protein molecules and elemental compositions are calculated. COMPOST also calculates mass to charge ratio values for protonated peptides expected from specified digests, locates specified amino acid subsequences or peptides of a specifIed molecular weight within a longer sequence, and predicts mass to charge ratio values for fragment ions from high-energy collision-induced dissociation of protonated peptides.     

Polarization consistent basis sets. V. The elements Si-Cl

Polarization consistent basis sets, optimized for density functional calculations, are proposed for the elements Si-Cl. Their performance for atomization energies, equilibrium geometries, harmonic vibrational frequencies, and associated infrared intensities is compared with other commonly used basis sets. Atomization energies can be predicted to within 0.01 kJ/mol per atom of the basis set limit by extrapolation of the pc-2, -3, and -4 results. Equilibrium bond distances and harmonic vibrational frequencies can be calculated to within 10(-5) A and 0.5 cm(-1), respectively, of the basis set limit. The pc-n basis sets are shown to give comparable or better accuracy than other alternatives, while containing fewer or equal number of primitive basis functions.     

New scale factors for harmonic vibrational frequencies using the B3LYP density functional method with the triple-zeta basis set 6-311+G(d,p)

We have calculated optimal frequency scaling factors for the B3LYP/ 6-311+G(d,p) method for fundamental vibrational frequencies on the basis of a set of 125 molecules. Using the new scaling factor, the vibrational frequencies calculated with the triple-zeta basis set 6-311+G(d,p) give significantly better accuracy than those calculated with the double-zeta 6-31G(d) basis set. Scale factors were also determined for low-frequency vibrations using the molecular set of 125 molecules and for zero-point energies using a smaller set of 40 molecules. We have studied the effect on the calculated vibrational frequencies for various combinations of diffuse and polarization functions added to the triple-zeta 6-311G basis set. The 6-311+G(d,p) basis set is found to give almost converged frequencies for most molecules, and we conclude that our optimum scaling factors are valid for the basis sets 6-311G(d,p) to 6-311++G(3df,3pd). The new scale factors are 0.9679 for vibrational frequencies, 1.0100 for low-frequency vibrations, and 0.9877 for zero-point vibrational energies.