Physical chemistry chemical physics : PCCP, Jan 7, 2016
The S66x8 dataset for noncovalent interactions of biochemical relevance has been re-examined by m... more The S66x8 dataset for noncovalent interactions of biochemical relevance has been re-examined by means of MP2-F12 and CCSD(F12*)(T) methods. We deem our revised benchmark data to be reliable to about 0.05 kcal mol(-1) RMS. Most levels of DFT perform quite poorly in the absence of dispersion corrections: somewhat surprisingly, that is even the case for the double hybrids and for dRPA75. Analysis of optimized D3BJ parameters reveals that the main benefit of dRPA75 and DSD double hybrids alike is the treatment of midrange dispersion. dRPA75-D3BJ is the best performer overall at RMSD = 0.10 kcal mol(-1). The nonlocal VV10 dispersion functional is especially beneficial for the double hybrids, particularly in DSD-PBEP86-NL (RMSD = 0.12 kcal mol(-1)). Other recommended dispersion-corrected functionals with favorable price/performance ratios are ωB97X-V, and, surprisingly, B3LYP-D3BJ and BLYP-D3BJ (RMSDs of 0.23, 0.20 and 0.23 kcal mol(-1), respectively). Without dispersion correction (but p...
The S66x8 dataset for noncovalent interactions of biochemical relevance has been re-examined by m... more The S66x8 dataset for noncovalent interactions of biochemical relevance has been re-examined by means of MP2-F12 and CCSD(F12*)(T) methods. We deem our revised benchmark data to be reliable to about 0.05 kcal mol À1 RMS. Most levels of DFT perform quite poorly in the absence of dispersion corrections: somewhat surprisingly, that is even the case for the double hybrids and for dRPA75. Analysis of optimized D3BJ parameters reveals that the main benefit of dRPA75 and DSD double hybrids alike is the treatment of midrange dispersion. dRPA75-D3BJ is the best performer overall at RMSD = 0.10 kcal mol À1 .
We have obtained uniform frequency scaling factors λ harm (for harmonic frequencies), λ fund (for... more We have obtained uniform frequency scaling factors λ harm (for harmonic frequencies), λ fund (for fundamentals), and λ ZPVE (for zero-point vibrational energies (ZPVEs)) for the Weigend−Ahlrichs and other selected basis sets for MP2, SCS-MP2, and a variety of DFT functionals including double hybrids. For selected levels of theory, we have also obtained scaling factors for true anharmonic fundamentals and ZPVEs obtained from quartic force fields. For harmonic frequencies, the double hybrids B2PLYP, B2GP-PLYP, and DSD-PBEP86 clearly yield the best performance at RMSD = 10−12 cm −1 for def2-TZVP and larger basis sets, compared to 5 cm −1 at the CCSD(T) basis set limit. For ZPVEs, again, the double hybrids are the best performers, reaching root-mean-square deviations (RMSDs) as low as 0.05 kcal/mol, but even mainstream functionals like B3LYP can get down to 0.10 kcal/mol. Explicitly anharmonic ZPVEs only are marginally more accurate. For fundamentals, however, simple uniform scaling is clearly inadequate.
There have been many theoretical studies of vibrational and electronic states of DNA bases. 1-3 T... more There have been many theoretical studies of vibrational and electronic states of DNA bases. 1-3 These are complicated by multiple lone pair electrons, limited symmetry, and possible tautomerism. Experimentally there have been many reports of absorption spectroscopy, ...
The basis set convergence of explicitly correlated ab initio methods, when applied to noncovalent... more The basis set convergence of explicitly correlated ab initio methods, when applied to noncovalent interactions, has been considered in the presence (and absence) of Boys-Bernardi counterpoise corrections, as well as using "half-counterpoise" (the average of raw and counterpoise-corrected values) as recently advocated in this journal [Burns, L. A.; Marshall, M. S.; Sherrill, C. D. J. Chem. Theory Comput. 2014, 10, 49-57]. Reference results were obtained using basis sets so large that BSSE (basis set superposition error) can be shown to be negligible. For the HF+CABS component, full counterpoise unequivocally exhibits the fastest basis set convergence. However, at the MP2-F12 and CCSD(T*)-F12b levels, surprisingly good uncorrected results can be obtained with small basis sets like cc-pVDZ-F12, owing to error compensation between basis set superposition error (which overbinds) and intrinsic basis set insufficiency (which underbinds). For intermediate sets like cc-pVTZ-F12, "half-half" averages work best, while for large basis sets like cc-pVQZ-F12, full counterpoise may be preferred but BSSE in uncorrected values is tolerably small for most purposes. A composite scheme in which CCSD(T)-MP2 "high level corrections" obtained at the CCSD(T*)-F12b/cc-pVDZ-F12 level are combined with "half-counterpoise" MP2-F12/cc-pVTZ-F12 interaction energies yields surprisingly good performance for standard benchmark sets like S22 and S66.
We have obtained uniform frequency scaling factors λharm (for harmonic frequencies), λfund (for f... more We have obtained uniform frequency scaling factors λharm (for harmonic frequencies), λfund (for fundamentals), and λZPVE (for zero-point vibrational energies (ZPVEs)) for the Weigend-Ahlrichs and other selected basis sets for MP2, SCS-MP2, and a variety of DFT functionals including double hybrids. For selected levels of theory, we have also obtained scaling factors for true anharmonic fundamentals and ZPVEs obtained from quartic force fields. For harmonic frequencies, the double hybrids B2PLYP, B2GP-PLYP, and DSD-PBEP86 clearly yield the best performance at RMSD = 10-12 cm(-1) for def2-TZVP and larger basis sets, compared to 5 cm(-1) at the CCSD(T) basis set limit. For ZPVEs, again, the double hybrids are the best performers, reaching root-mean-square deviations (RMSDs) as low as 0.05 kcal/mol, but even mainstream functionals like B3LYP can get down to 0.10 kcal/mol. Explicitly anharmonic ZPVEs only are marginally more accurate. For fundamentals, however, simple uniform scaling is c...
Experimental and theoretical investigations of ultrafast processes in molecules or clusters can l... more Experimental and theoretical investigations of ultrafast processes in molecules or clusters can lead to a detailed understanding of the dynamical processes involved. Their control by tailored laser pulses can be employed to determine how the interplay of size, structures and light fields can be used to manipulate optical properties and chemical reactivity of these systems. Moreover, laserselective femtochemistry [1–11] can
ABSTRACT A modification of the semi-empirical PM3 electronic structure method is proposed. It emp... more ABSTRACT A modification of the semi-empirical PM3 electronic structure method is proposed. It employs a coordinate scaling procedure, such that the harmonic frequencies from the modified PM3 potentials for lower-energy conformers of glycine (conformer I), alanine (conformers I and II) and proline (conformer II), fit more closely with ab initio (MP2/DZP) harmonic frequencies. The anharmonic frequencies are then calculated using the modified PM3 surfaces with the Vibrational Self-Consistent Field (VSCF) and Correlation-Corrected VSCF (CC-VSCF) methods. The computed anharmonic frequencies are in very good accord with spectroscopic experiments for the three amino acids. The results are much superior to those obtained from standard (unscaled) PM3 potentials, indicating that the modified PM3 potentials may be used as high quality potentials for biological molecules, at least in the configuration ranges pertinent to vibrational spectroscopy. The scaling parameters computed for the lowest energy conformers listed above were tested for transferability: they were used in computing the anharmonic spectra of two other conformers (glycine II and proline I). The good agreement of the resulting frequencies with observed frequencies, indicates the transferability of the scaling parameters. It is concluded from this study that the improved PM3 potentials offer accurate and computationally efficient force fields for vibrational spectroscopy calculations of biological molecules. Possible additional applications of the new potentials are discussed.
The results of harmonic and anharmonic frequency calculations on a guanine-cytosine complex with ... more The results of harmonic and anharmonic frequency calculations on a guanine-cytosine complex with an enolic structure (a tautomeric form with cytosine in the enol form and with a hydrogen at the 7-position on guanine) are presented and compared to gas-phase IR-UV double resonance spectral data. Harmonic frequencies were obtained at the RI-MP2/cc-pVDZ, RI-MP2/TZVPP, and semiempirical PM3 levels of electronic structure theory. Anharmonic frequencies were obtained by the CC-VSCF method with improved PM3 potential surfaces; the improved PM3 potential surfaces are obtained from standard PM3 theory by coordinate scaling such that the improved PM3 harmonic frequencies are the same as those computed at the RI-MP2/cc-pVDZ level. Comparison of the data with experimental results indicates that the average absolute percentage deviation for the methods is 2.6% for harmonic RI-MP2/cc-pVDZ (3.0% with the inclusion of a 0.956 scaling factor that compensates for anharmonicity), 2.5% for harmonic RI-MP2/TZVPP (2.9% with a 0.956 anharmonicity factor included), and 2.3% for adapted PM3 CC-VSCF; the empirical scaling factor for the ab initio harmonic calculations improves the stretching frequencies but decreases the accuracy of the other mode frequencies. The agreement with experiment supports the adequacy of the improved PM3 potentials for describing the anharmonic force field of the G...C base pair in the spectroscopically probed region. These results may be useful for the prediction of the pathways of vibrational energy flow upon excitation of this system. The anharmonic calculations indicate that anharmonicity along single mode coordinates can be significant for simple stretching modes. For several other cases, coupling between different vibrational modes provides the main contribution to anharmonicity. Examples of strongly anharmonically coupled modes are the symmetric stretch and group torsion of the hydrogen-bonded NH2 group on guanine, the OH stretch and torsion of the enol group on cytosine, and the NH stretch and NH out-of-plane bend of the non-hydrogen-bonded NH group on guanine.
The anharmonic vibrational spectra of α-D-glucose, β-D-glucose, and sucrose are computed by the v... more The anharmonic vibrational spectra of α-D-glucose, β-D-glucose, and sucrose are computed by the vibrational self-consistent field (VSCF) method, using potential energy surfaces from electronic structure theory, for the lowest energy conformers that correspond to the gas phase and to the crystalline phase, respectively. The results are compared with ultraviolet-infrared (UV-IR) spectra of phenyl β-D-glucopyranoside in a molecular beam, with literature results for sugars in matrices and with new experimental data for the crystalline state. Car-Parrinello dynamics simulations are also used to study temperature effects on the spectra of α-D-glucose and β-D-glucose and to predict their vibrational spectra at 50, 150, and 300 K. The effects of temperature on the spectral features are analyzed and compared with results of the VSCF calculations conducted at 0 K. The main results include: (i) new potential surfaces, constructed from Hartree-Fock, adjusted to fit harmonic frequencies from Møller-Plesset (MP2) calculations, that give very good agreement with gas phase, matrix, and solid state spectra; (ii) computed infrared spectra of the crystalline solid of α-glucose, which are substantially improved by including mimic groups that represent the effect of the solid environment on the sugar; and (iii) identification of a small number of combination-mode transitions, which are predicted to be strong enough for experimental observation. The results are used to assess the role of anharmonic effects in the spectra of the sugars in isolation and in the solid state and to discuss the spectroscopic accuracy of potentials from different electronic structure methods.
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2008
The vibrational spectrum of triacetone triperoxide (TATP) is studied by the correlation-corrected... more The vibrational spectrum of triacetone triperoxide (TATP) is studied by the correlation-corrected vibrational self-consistent field (CC-VSCF) method which incorporates anharmonic effects. Fundamental, overtone, and combination band frequencies are obtained by using a potential based on the PM3 method and yielding the same harmonic frequencies as DFT/cc-pVDZ calculations. Fundamentals and overtones are also studied with anharmonic single-mode (without coupling) DFT/cc-pVDZ calculations. Average deviations from experiment are similar for all methods: 2.1-2.5%. Groups of degenerate vibrations form regions of numerous combination bands with low intensity: the 5600-5800 cm(-1) region contains ca. 70 overtones and combinations of CH stretches. Anharmonic interactions are analyzed.
Molecular dynamics (MD) simulations are carried out for the complex of glucose with KNO(3) and fo... more Molecular dynamics (MD) simulations are carried out for the complex of glucose with KNO(3) and for complexes of the type glucose-KNO(3)-(H(2)O)(n), for n < or = 11. Structure and dynamic properties of the systems are explored. The MD simulations are carried out using primarily the DL_POLY/OPLS force field, and global and local minimum energy structures of some of the systems are compared with ab initio calculations. The main findings include: (1) complexation with KNO(3) leads to an "inverse anomeric effect", with the beta-glucose complex more stable than the alpha-glucose by approximately 1.74 kcal mol(-1); (2) as temperature is increased to 600 K, the KNO(3) remains undissociated in the 1 : 1 complex, with the K(+) hooked to the equilibrium site, and the NO(3)(-) bound to it, undergoing large-amplitude bending/torsional motions; (3) for n > or = 3 water molecules added to the system, charge separation into K(+) and NO(3)(-) ions takes place; (4) for the sugar-water system with n = 11 water molecules all hydroxyl groups are hydrated with the glucose adopting a surface position, indicative of a surfactant property of the sugar; and (5) comparison of DL_POLY with MP2/TZP structure predictions indicates that the empirical force field predicts global and local minimum structures reasonably well, but errs in giving the energy rankings of the different minima. The implications of the results on the effects of salts on saccharides are discussed.
The experimental mid- and far-IR spectra of six conformers of phenylalanine in the gas phase are ... more The experimental mid- and far-IR spectra of six conformers of phenylalanine in the gas phase are presented. The experimental spectra are compared to spectra calculated at the B3LYP and at the MP2 level. The differences between B3LYP and MP2 IR spectra are found to be small. The agreement between experiment and theory is generally found to be very good, however strong discrepancies exist when -NH2 out-of-plane vibrations are involved. The relative energies of the minima as well as of some transition states connecting the minima are explored at the CCSD(T) level. Most transition states are found to be less than 2000 cm(-1) above the lowest energy structure. A simple model to describe the observed conformer abundances based on quasi-equilibria near the barriers is presented and it appears to describe the experimental observation reasonably well. In addition, the vibrations of one of the conformers are investigated using the correlation-corrected vibrational self-consistent field method.
The role of anharmonic effects in the vibrational spectroscopy of small biological molecules and ... more The role of anharmonic effects in the vibrational spectroscopy of small biological molecules and their 1 : 1 complexes with water is discussed. The strengths and limitations of the vibrational self-consistent field (VSCF) method and its extensions as a computational tool for this purpose are examined. Anharmonic coupling between different vibrational modes is found to be very important for these systems, even for fundamental transitions, and incorporation of these effects seems essential for quantitative interpretation of experimental data. Both analytical, empirical force fields, and potential surfaces computed from electronic structure methods are used in VSCF calculations of several benchmark systems and compared with experimental spectroscopic data. Glycine in several conformers, the glycine-water complex, and N-methylacetamide are among the systems discussed. The main conclusions are: (1) Electronic structure methods such as MP2/DZP and density functional B97, give very good agreement with experimental data. Thus, MP2 and B97 clearly provide an accurate description of the anharmonic interactions. VSCF calculations, including all modes, with MP2, B97 and other successful methods are presently feasible for molecules with up to 15-20 atoms. (2) The electronic structure methods seem to give spectroscopic predictions in much better accord with experiment than standard empirical force fields such as AMBER or OPLS. The anharmonic couplings provided by these methods differ greatly, in the cases tested to date, from the ab initio ones. The implications of these results for future modeling of small biomolecules are discussed. Comments are provided on future directions in this subject, including extensions to large biomolecules.
... Lett. Corresponding authors: (IB) E-mail: [email protected] (RBG) E-mail: [email protected] 1.... more ... Lett. Corresponding authors: (IB) E-mail: [email protected] (RBG) E-mail: [email protected] 1. Introduction Vibrational spectra make available the patterns, reflecting the characteristic vibrations in molecules. ... [10] B. Brauer, M. Pincu, V. Buch, I. Bar, JP Simons, RB Gerber, J. Phys. ...
The infrared spectrum of N-phenylpyrrole (PP) was measured in the gas phase and in an argon matri... more The infrared spectrum of N-phenylpyrrole (PP) was measured in the gas phase and in an argon matrix, and the Raman spectrum was obtained in a single crystal. The measured matrix shifts are found to be small: many bands are not split, and the shifts from the gas phase values are less than 1%. Splitting to two sub-bands is observed for
Physical chemistry chemical physics : PCCP, Jan 7, 2016
The S66x8 dataset for noncovalent interactions of biochemical relevance has been re-examined by m... more The S66x8 dataset for noncovalent interactions of biochemical relevance has been re-examined by means of MP2-F12 and CCSD(F12*)(T) methods. We deem our revised benchmark data to be reliable to about 0.05 kcal mol(-1) RMS. Most levels of DFT perform quite poorly in the absence of dispersion corrections: somewhat surprisingly, that is even the case for the double hybrids and for dRPA75. Analysis of optimized D3BJ parameters reveals that the main benefit of dRPA75 and DSD double hybrids alike is the treatment of midrange dispersion. dRPA75-D3BJ is the best performer overall at RMSD = 0.10 kcal mol(-1). The nonlocal VV10 dispersion functional is especially beneficial for the double hybrids, particularly in DSD-PBEP86-NL (RMSD = 0.12 kcal mol(-1)). Other recommended dispersion-corrected functionals with favorable price/performance ratios are ωB97X-V, and, surprisingly, B3LYP-D3BJ and BLYP-D3BJ (RMSDs of 0.23, 0.20 and 0.23 kcal mol(-1), respectively). Without dispersion correction (but p...
The S66x8 dataset for noncovalent interactions of biochemical relevance has been re-examined by m... more The S66x8 dataset for noncovalent interactions of biochemical relevance has been re-examined by means of MP2-F12 and CCSD(F12*)(T) methods. We deem our revised benchmark data to be reliable to about 0.05 kcal mol À1 RMS. Most levels of DFT perform quite poorly in the absence of dispersion corrections: somewhat surprisingly, that is even the case for the double hybrids and for dRPA75. Analysis of optimized D3BJ parameters reveals that the main benefit of dRPA75 and DSD double hybrids alike is the treatment of midrange dispersion. dRPA75-D3BJ is the best performer overall at RMSD = 0.10 kcal mol À1 .
We have obtained uniform frequency scaling factors λ harm (for harmonic frequencies), λ fund (for... more We have obtained uniform frequency scaling factors λ harm (for harmonic frequencies), λ fund (for fundamentals), and λ ZPVE (for zero-point vibrational energies (ZPVEs)) for the Weigend−Ahlrichs and other selected basis sets for MP2, SCS-MP2, and a variety of DFT functionals including double hybrids. For selected levels of theory, we have also obtained scaling factors for true anharmonic fundamentals and ZPVEs obtained from quartic force fields. For harmonic frequencies, the double hybrids B2PLYP, B2GP-PLYP, and DSD-PBEP86 clearly yield the best performance at RMSD = 10−12 cm −1 for def2-TZVP and larger basis sets, compared to 5 cm −1 at the CCSD(T) basis set limit. For ZPVEs, again, the double hybrids are the best performers, reaching root-mean-square deviations (RMSDs) as low as 0.05 kcal/mol, but even mainstream functionals like B3LYP can get down to 0.10 kcal/mol. Explicitly anharmonic ZPVEs only are marginally more accurate. For fundamentals, however, simple uniform scaling is clearly inadequate.
There have been many theoretical studies of vibrational and electronic states of DNA bases. 1-3 T... more There have been many theoretical studies of vibrational and electronic states of DNA bases. 1-3 These are complicated by multiple lone pair electrons, limited symmetry, and possible tautomerism. Experimentally there have been many reports of absorption spectroscopy, ...
The basis set convergence of explicitly correlated ab initio methods, when applied to noncovalent... more The basis set convergence of explicitly correlated ab initio methods, when applied to noncovalent interactions, has been considered in the presence (and absence) of Boys-Bernardi counterpoise corrections, as well as using "half-counterpoise" (the average of raw and counterpoise-corrected values) as recently advocated in this journal [Burns, L. A.; Marshall, M. S.; Sherrill, C. D. J. Chem. Theory Comput. 2014, 10, 49-57]. Reference results were obtained using basis sets so large that BSSE (basis set superposition error) can be shown to be negligible. For the HF+CABS component, full counterpoise unequivocally exhibits the fastest basis set convergence. However, at the MP2-F12 and CCSD(T*)-F12b levels, surprisingly good uncorrected results can be obtained with small basis sets like cc-pVDZ-F12, owing to error compensation between basis set superposition error (which overbinds) and intrinsic basis set insufficiency (which underbinds). For intermediate sets like cc-pVTZ-F12, "half-half" averages work best, while for large basis sets like cc-pVQZ-F12, full counterpoise may be preferred but BSSE in uncorrected values is tolerably small for most purposes. A composite scheme in which CCSD(T)-MP2 "high level corrections" obtained at the CCSD(T*)-F12b/cc-pVDZ-F12 level are combined with "half-counterpoise" MP2-F12/cc-pVTZ-F12 interaction energies yields surprisingly good performance for standard benchmark sets like S22 and S66.
We have obtained uniform frequency scaling factors λharm (for harmonic frequencies), λfund (for f... more We have obtained uniform frequency scaling factors λharm (for harmonic frequencies), λfund (for fundamentals), and λZPVE (for zero-point vibrational energies (ZPVEs)) for the Weigend-Ahlrichs and other selected basis sets for MP2, SCS-MP2, and a variety of DFT functionals including double hybrids. For selected levels of theory, we have also obtained scaling factors for true anharmonic fundamentals and ZPVEs obtained from quartic force fields. For harmonic frequencies, the double hybrids B2PLYP, B2GP-PLYP, and DSD-PBEP86 clearly yield the best performance at RMSD = 10-12 cm(-1) for def2-TZVP and larger basis sets, compared to 5 cm(-1) at the CCSD(T) basis set limit. For ZPVEs, again, the double hybrids are the best performers, reaching root-mean-square deviations (RMSDs) as low as 0.05 kcal/mol, but even mainstream functionals like B3LYP can get down to 0.10 kcal/mol. Explicitly anharmonic ZPVEs only are marginally more accurate. For fundamentals, however, simple uniform scaling is c...
Experimental and theoretical investigations of ultrafast processes in molecules or clusters can l... more Experimental and theoretical investigations of ultrafast processes in molecules or clusters can lead to a detailed understanding of the dynamical processes involved. Their control by tailored laser pulses can be employed to determine how the interplay of size, structures and light fields can be used to manipulate optical properties and chemical reactivity of these systems. Moreover, laserselective femtochemistry [1–11] can
ABSTRACT A modification of the semi-empirical PM3 electronic structure method is proposed. It emp... more ABSTRACT A modification of the semi-empirical PM3 electronic structure method is proposed. It employs a coordinate scaling procedure, such that the harmonic frequencies from the modified PM3 potentials for lower-energy conformers of glycine (conformer I), alanine (conformers I and II) and proline (conformer II), fit more closely with ab initio (MP2/DZP) harmonic frequencies. The anharmonic frequencies are then calculated using the modified PM3 surfaces with the Vibrational Self-Consistent Field (VSCF) and Correlation-Corrected VSCF (CC-VSCF) methods. The computed anharmonic frequencies are in very good accord with spectroscopic experiments for the three amino acids. The results are much superior to those obtained from standard (unscaled) PM3 potentials, indicating that the modified PM3 potentials may be used as high quality potentials for biological molecules, at least in the configuration ranges pertinent to vibrational spectroscopy. The scaling parameters computed for the lowest energy conformers listed above were tested for transferability: they were used in computing the anharmonic spectra of two other conformers (glycine II and proline I). The good agreement of the resulting frequencies with observed frequencies, indicates the transferability of the scaling parameters. It is concluded from this study that the improved PM3 potentials offer accurate and computationally efficient force fields for vibrational spectroscopy calculations of biological molecules. Possible additional applications of the new potentials are discussed.
The results of harmonic and anharmonic frequency calculations on a guanine-cytosine complex with ... more The results of harmonic and anharmonic frequency calculations on a guanine-cytosine complex with an enolic structure (a tautomeric form with cytosine in the enol form and with a hydrogen at the 7-position on guanine) are presented and compared to gas-phase IR-UV double resonance spectral data. Harmonic frequencies were obtained at the RI-MP2/cc-pVDZ, RI-MP2/TZVPP, and semiempirical PM3 levels of electronic structure theory. Anharmonic frequencies were obtained by the CC-VSCF method with improved PM3 potential surfaces; the improved PM3 potential surfaces are obtained from standard PM3 theory by coordinate scaling such that the improved PM3 harmonic frequencies are the same as those computed at the RI-MP2/cc-pVDZ level. Comparison of the data with experimental results indicates that the average absolute percentage deviation for the methods is 2.6% for harmonic RI-MP2/cc-pVDZ (3.0% with the inclusion of a 0.956 scaling factor that compensates for anharmonicity), 2.5% for harmonic RI-MP2/TZVPP (2.9% with a 0.956 anharmonicity factor included), and 2.3% for adapted PM3 CC-VSCF; the empirical scaling factor for the ab initio harmonic calculations improves the stretching frequencies but decreases the accuracy of the other mode frequencies. The agreement with experiment supports the adequacy of the improved PM3 potentials for describing the anharmonic force field of the G...C base pair in the spectroscopically probed region. These results may be useful for the prediction of the pathways of vibrational energy flow upon excitation of this system. The anharmonic calculations indicate that anharmonicity along single mode coordinates can be significant for simple stretching modes. For several other cases, coupling between different vibrational modes provides the main contribution to anharmonicity. Examples of strongly anharmonically coupled modes are the symmetric stretch and group torsion of the hydrogen-bonded NH2 group on guanine, the OH stretch and torsion of the enol group on cytosine, and the NH stretch and NH out-of-plane bend of the non-hydrogen-bonded NH group on guanine.
The anharmonic vibrational spectra of α-D-glucose, β-D-glucose, and sucrose are computed by the v... more The anharmonic vibrational spectra of α-D-glucose, β-D-glucose, and sucrose are computed by the vibrational self-consistent field (VSCF) method, using potential energy surfaces from electronic structure theory, for the lowest energy conformers that correspond to the gas phase and to the crystalline phase, respectively. The results are compared with ultraviolet-infrared (UV-IR) spectra of phenyl β-D-glucopyranoside in a molecular beam, with literature results for sugars in matrices and with new experimental data for the crystalline state. Car-Parrinello dynamics simulations are also used to study temperature effects on the spectra of α-D-glucose and β-D-glucose and to predict their vibrational spectra at 50, 150, and 300 K. The effects of temperature on the spectral features are analyzed and compared with results of the VSCF calculations conducted at 0 K. The main results include: (i) new potential surfaces, constructed from Hartree-Fock, adjusted to fit harmonic frequencies from Møller-Plesset (MP2) calculations, that give very good agreement with gas phase, matrix, and solid state spectra; (ii) computed infrared spectra of the crystalline solid of α-glucose, which are substantially improved by including mimic groups that represent the effect of the solid environment on the sugar; and (iii) identification of a small number of combination-mode transitions, which are predicted to be strong enough for experimental observation. The results are used to assess the role of anharmonic effects in the spectra of the sugars in isolation and in the solid state and to discuss the spectroscopic accuracy of potentials from different electronic structure methods.
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2008
The vibrational spectrum of triacetone triperoxide (TATP) is studied by the correlation-corrected... more The vibrational spectrum of triacetone triperoxide (TATP) is studied by the correlation-corrected vibrational self-consistent field (CC-VSCF) method which incorporates anharmonic effects. Fundamental, overtone, and combination band frequencies are obtained by using a potential based on the PM3 method and yielding the same harmonic frequencies as DFT/cc-pVDZ calculations. Fundamentals and overtones are also studied with anharmonic single-mode (without coupling) DFT/cc-pVDZ calculations. Average deviations from experiment are similar for all methods: 2.1-2.5%. Groups of degenerate vibrations form regions of numerous combination bands with low intensity: the 5600-5800 cm(-1) region contains ca. 70 overtones and combinations of CH stretches. Anharmonic interactions are analyzed.
Molecular dynamics (MD) simulations are carried out for the complex of glucose with KNO(3) and fo... more Molecular dynamics (MD) simulations are carried out for the complex of glucose with KNO(3) and for complexes of the type glucose-KNO(3)-(H(2)O)(n), for n < or = 11. Structure and dynamic properties of the systems are explored. The MD simulations are carried out using primarily the DL_POLY/OPLS force field, and global and local minimum energy structures of some of the systems are compared with ab initio calculations. The main findings include: (1) complexation with KNO(3) leads to an "inverse anomeric effect", with the beta-glucose complex more stable than the alpha-glucose by approximately 1.74 kcal mol(-1); (2) as temperature is increased to 600 K, the KNO(3) remains undissociated in the 1 : 1 complex, with the K(+) hooked to the equilibrium site, and the NO(3)(-) bound to it, undergoing large-amplitude bending/torsional motions; (3) for n > or = 3 water molecules added to the system, charge separation into K(+) and NO(3)(-) ions takes place; (4) for the sugar-water system with n = 11 water molecules all hydroxyl groups are hydrated with the glucose adopting a surface position, indicative of a surfactant property of the sugar; and (5) comparison of DL_POLY with MP2/TZP structure predictions indicates that the empirical force field predicts global and local minimum structures reasonably well, but errs in giving the energy rankings of the different minima. The implications of the results on the effects of salts on saccharides are discussed.
The experimental mid- and far-IR spectra of six conformers of phenylalanine in the gas phase are ... more The experimental mid- and far-IR spectra of six conformers of phenylalanine in the gas phase are presented. The experimental spectra are compared to spectra calculated at the B3LYP and at the MP2 level. The differences between B3LYP and MP2 IR spectra are found to be small. The agreement between experiment and theory is generally found to be very good, however strong discrepancies exist when -NH2 out-of-plane vibrations are involved. The relative energies of the minima as well as of some transition states connecting the minima are explored at the CCSD(T) level. Most transition states are found to be less than 2000 cm(-1) above the lowest energy structure. A simple model to describe the observed conformer abundances based on quasi-equilibria near the barriers is presented and it appears to describe the experimental observation reasonably well. In addition, the vibrations of one of the conformers are investigated using the correlation-corrected vibrational self-consistent field method.
The role of anharmonic effects in the vibrational spectroscopy of small biological molecules and ... more The role of anharmonic effects in the vibrational spectroscopy of small biological molecules and their 1 : 1 complexes with water is discussed. The strengths and limitations of the vibrational self-consistent field (VSCF) method and its extensions as a computational tool for this purpose are examined. Anharmonic coupling between different vibrational modes is found to be very important for these systems, even for fundamental transitions, and incorporation of these effects seems essential for quantitative interpretation of experimental data. Both analytical, empirical force fields, and potential surfaces computed from electronic structure methods are used in VSCF calculations of several benchmark systems and compared with experimental spectroscopic data. Glycine in several conformers, the glycine-water complex, and N-methylacetamide are among the systems discussed. The main conclusions are: (1) Electronic structure methods such as MP2/DZP and density functional B97, give very good agreement with experimental data. Thus, MP2 and B97 clearly provide an accurate description of the anharmonic interactions. VSCF calculations, including all modes, with MP2, B97 and other successful methods are presently feasible for molecules with up to 15-20 atoms. (2) The electronic structure methods seem to give spectroscopic predictions in much better accord with experiment than standard empirical force fields such as AMBER or OPLS. The anharmonic couplings provided by these methods differ greatly, in the cases tested to date, from the ab initio ones. The implications of these results for future modeling of small biomolecules are discussed. Comments are provided on future directions in this subject, including extensions to large biomolecules.
... Lett. Corresponding authors: (IB) E-mail: [email protected] (RBG) E-mail: [email protected] 1.... more ... Lett. Corresponding authors: (IB) E-mail: [email protected] (RBG) E-mail: [email protected] 1. Introduction Vibrational spectra make available the patterns, reflecting the characteristic vibrations in molecules. ... [10] B. Brauer, M. Pincu, V. Buch, I. Bar, JP Simons, RB Gerber, J. Phys. ...
The infrared spectrum of N-phenylpyrrole (PP) was measured in the gas phase and in an argon matri... more The infrared spectrum of N-phenylpyrrole (PP) was measured in the gas phase and in an argon matrix, and the Raman spectrum was obtained in a single crystal. The measured matrix shifts are found to be small: many bands are not split, and the shifts from the gas phase values are less than 1%. Splitting to two sub-bands is observed for
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Papers by B. Brauer