Implementation of a graphical user interface for the virtual multifrequency spectrometer: The...

Implementation of a Graphical User Interface for theVirtual Multifrequency Spectrometer: The VMS-Draw Tool

Daniele Licari,[a] Alberto Baiardi,[a] Malgorzata Biczysko,[a,b] Franco Egidi,[a]

Camille Latouche,[a] and Vincenzo Barone*[a]

This article presents the setup and implementation of a graph-

ical user interface (VMS-Draw) for a virtual multifrequency

spectrometer. Special attention is paid to ease of use, general-

ity and robustness for a panel of spectroscopic techniques and

quantum mechanical approaches. Depending on the kind of

data to be analyzed, VMS-Draw produces different types of

graphical representations, including two-dimensional or three-

dimesional (3D) plots, bar charts, or heat maps. Among other

integrated features, one may quote the convolution of stick

spectra to obtain realistic line-shapes. It is also possible to ana-

lyze and visualize, together with the structure, the molecular

orbitals and/or the vibrational motions of molecular systems

thanks to 3D interactive tools. On these grounds, VMS-Draw

could represent a useful additional tool for spectroscopic stud-

ies integrating measurements and computer simulations.

VC 2014 Wiley Periodicals, Inc.

DOI: 10.1002/jcc.23785

Introduction

Nowadays, spectroscopic techniques can provide qualitative

and quantitative information on the physical-chemical proper-

ties of molecular systems in different environments. However,

the complexity and variety of these systems make it very diffi-

cult to unambiguously interpret the experimental data, that is,

to identify which species are present in a sample, and to

determine their relative population, their structure and the

interactions with surroundings, and how these factors contrib-

ute to the generation of the spectroscopic response.[1–3] Elec-

tronic structure codes (ESC) are providing remarkable aid in

this connection in view of the increasing reliability of the

results also for medium- to large size-systems both in gas and

in condensed phases. However, interpretation and comparison

of experimental and theoretical data is becoming more and

more difficult in view of the increasing dimensions and com-

plexity of the studied systems, not to mention the subtle inter-

play of stereoelectronic, dynamical and environmental effects,

whose disentanglement requires specific tools.[4–7] All those

factors prompted our group to develop a virtual multifre-

quency spectrometer (VMS) providing user-friendly access to

the latest developments of computational spectroscopy also

to nonspecialists.[8] In this framework, a suitable graphical user

interface (GUI) can offer an invaluable aid in preorganizing and

presenting in a more direct way the information produced by

measurements and/or computations focusing attention on the

underlying physical-chemical features without being con-

cerned with technical details. A number of graphic engines

(e.g., GaussView,[9] Avogadro,[10] GaussSum,[11] PyVib,[12] and

Gabedit[13]), or simple command lines (Swizard/AOMix[14,15])

can be already interfaced to several ESCs (for instance, the

Gaussian package,[16] which will be our reference source of

spectroscopic quantities) for purposes of data preparation, vis-

ualization, and analysis. However, none of these engines offers

all the characteristics we consider mandatory for a flexible

user-friendly graphical tool devoted to computational spec-

troscopy and including both general utilities for

experimentally-oriented scientists and advanced tools for theo-

reticians and developers. Among features not yet available, we

can mention the possibility of plotting anharmonic vibrational

spectra, vibrationally resolved electronic spectra, resonance

Raman (RR) spectra, not to speak about normalization, conver-

sion and other manipulations of several spectra at the same

time. To address these aspects, we are adding to the computa-

tional part of VMS (hereafter, VMS-Comp) a new all-in-one GUI

(hereafter VMS-Draw) with the goal of standardizing results,

increasing the productivity of both computationally and

experimentally-oriented researchers, and allowing an easier

and faster sharing of results, in all the significant ranges of the

electromagnetic field. In the following sections, after a short

presentation of the general philosophy and of some technical

aspects, we will discuss in more detail the key features of

VMS-Draw, with special focus on vibrational and electronic

spectroscopies.

General Philosophy and Technical Aspects

As mentioned in the introduction, the spectroscopic quantities

obtained by ESCs must be further processed before becoming

suitable for graphical representation and/or vis-a-vis

[a] D. Licari, A. Baiardi, M. Biczysko, F. Egidi, C. Latouche, V. Barone

Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy

E-mail: [email protected]

[b] M. Biczysko

Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti

OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G.

Moruzzi 1, I-56124 Pisa, Italy

Contract grant sponsor: European Union’s Seventh Framework

Programme (FP7/2007-2013); Contract grant number: ERC-2012-AdG-

320951-DREAMS.

VC 2014 Wiley Periodicals, Inc.

Journal of Computational Chemistry 2014, DOI: 10.1002/jcc.23785 1

SOFTWARE NEWS AND UPDATESWWW.C-CHEM.ORG

http://onlinelibrary.wiley.com/

comparison with experimental spectra. In our VMS project (see

Fig. 1) this task is performed by a dedicated tool (VMS-Comp)

able to read data issuing from different ESCs and to compute

vibrational, electronic (possibly vibrationally resolved), elec-

tronic spin resonance (ESR), or microwave (MW) spectra.

Improvements of VMS-Comp and inclusion of additional spec-

troscopies are under way in our group.

Next, VMS-Draw was devised with the aim of integrating

powerful multiplatform user-friendly graphical tools able to

analyze, compare, and visualize all the spectroscopic properties

that can be obtained from last generation ESCs. The new GUI

can recognize several types of numerical inputs thanks to ad

hoc file formats and is optimized to manage heterogeneous

data sets (e.g., images of different graphical formats, textual

representations or direct outputs from VMS-Comp).

In addition, VMS-Draw can retrieve, analyze, and compare

the computational results and experimental data stored in the

system to integrate art and science (SIAS).[17] SIAS is a new

interactive system for diagnostic and preservation of artworks

and it allows the user to archive, consult, share, analyze, and

enrich scientific and humanistic contents related to cultural

heritage. VMS-Draw allows a more accurate consultation and

analysis of spectroscopic data stored in SIAS by accessing its

database via Web services.

Depending on the specific data set to be analyzed, VMS-

Draw is able to produce different graphical representations,

like two-dimensional (2D) or three-dimensional (3D) plots, bar

charts, heat maps, and others (see Fig. 2). It is, of course, possi-

ble to produce journal-quality scientific graphs and export

them in high-resolution graphics formats such as scalable vec-

tor graphics or portable network graphics. The plots can be

highly customized by a number of settable parameters, includ-

ing graphical properties and other features, like, e.g., fonts, col-

ors, size and line styles. Finally, multiple 2D spectra plots can

be merged automatically into a single high-resolution image.

A special file format (VMS Project format) is implemented to

keep all the data of the current project in a single file, which

can be always opened to restart working on the saved docu-

ment at any time. On opening of an output file from a quan-

tum mechanical (QM) calculation, VMS-Draw immediately

parses all the internal data and lists the operations which can

be performed for the selected calculation.

To optimize portability, VMS-Draw has been written in the

Java programming language, and includes three open-source

Java applications (Jmol,[18] Jamberoo[19] and Plot Digitizer[20])

running on Windows, MacOSX, and Unix/Linux operating sys-

tems, which allow the user to manipulate and visualize 3D

structures loaded from ESCs or dedicated databases.

VMS-Draw uses several open-source libraries such as Jfree-

chart[21] to display professional quality charts, Filedrop[22] to

drag and drop files into the Java program, the VectorGraphics

package of the FreeHEP Java Library[23] to export to a variety

Figure 1. The new VMS-Draw GUI in the framework of the whole VMS project.

SOFTWARE NEWS AND UPDATES WWW.C-CHEM.ORG

2 Journal of Computational Chemistry 2014, DOI: 10.1002/jcc.23785 WWW.CHEMISTRYVIEWS.COM

image formats, XStream[24] to serialize objects to XML and

back again, SwingX,[25] which contains extensions to the Swing

GUI toolkit and RSyntaxTextArea[26] that provides a code fold-

ing text components written in Swing.

Finally, multithreads algorithms are used to optimize the

handling of large data sets and dynamic tab navigation is con-

sistently used to allow the creation of tabs with different

graphical tools that can be easily added or removed.

Generic Spectra and Common Features

As mentioned before, VMS-Draw provides an integrated envi-

ronment for direct comparison between different types of the-

oretical and experimental spectra, allowing several

manipulations like shifting and rescaling. Furthermore, several

computed spectra can be combined in a weighted mixture to

better reproduce the experimental conditions. Finally, VMS-

Draw may be used as a general-purpose tool for the analysis,

visualization, and presentation of scientific data. A new input

file format was designed for use with a generic data source,

which is independent of any QM code. It may contain any sub-

set of the supported data, with data types categorized as

spectra, vectors, matrices, and surfaces, which are represented

by charts, heat maps and 2D or 3D plots. Figure 3 summarizes

the main features of our software.

A dedicated tool offers the possibility to plot several spectra

on the same frame. From the practical point of view, the choice

could be to import all the spectra at the same time or to add

them one by one. As an example, Figure 4 shows how it is sim-

ple to compare the optical properties of a whole set of mole-

cules, here of p-Phenylene bis-imidazoles (with para-p-: Me,

OMe, CN).

Moreover if several species (e.g., conformers or tautomeric

forms) can coexist under experimental conditions, they all con-

tribute to the overall spectrum line-shape. Such effects can be

simulated with VMS-Draw, taking into account the relative

population of the different species. In principle, there are sev-

eral possibilities to evaluate the composition of a complex

molecular mixture. A first option is to simulate fully ab initio

spectra, with single contributions estimated from Boltzman

populations obtained, in turn, from more- or less-sophisticated

computations of free energies (see e.g. Refs. [27,28], for defini-

tion and application of elaborate theoretical models). Alterna-

tively, the percentages of different species can be estimated

by the analysis of some relevant features of experimental spec-

tra and then used to simulate overall band shapes.[29] It is also

possible to estimate relative amounts of subcomponents by

fitting theoretical spectra (varying the contributions of single-

components) to the observed experimental data. In all cases

such an analysis is facilitated by a graphical tool included into

VMS-Draw, which allows both inclusion of accurate data for

relative populations (as an example the IR spectrum of gly-

cine[28] is shown Fig. 5), as well as manual modification of the

percentages of different species.

Figure 2. Sketch of the different plots produced by VMS-Draw depending on runtime settings.




It is also possible to tune the shape of the spectra according

to the line width. Furthermore, VMS-Draw is able to plot sev-

eral spectra at the same time, possibly together with the stick

representation of single transitions. As an example, in Figure 6,

are shown both absorption (blue) and emission (red) simulated

spectra of Me-Phenylene bis-imidazoles using vertical excita-

tions convoluted by Gaussian functions. It is quite apparent

that both spectra have the same intensity maxima, thanks to

the normalization tool available in VMS-Draw. This latter fea-

ture allows the user to directly compare the optical properties

of compounds, clearly showing the Stokes shift even for transi-

tions with small oscillator strengths.

VMS-Draw allows theoretical spectra to be directly com-

pared with their experimental counterparts (see Fig. 7) possi-

bly imported in a numerical format (xy file with columns

corresponding to energies and intensities) or digitized from

the available graphical source (in gif, jpg or png format). As

often intensities of experimental spectra are reported in arbi-

trary units both spectra can be normalized for easier compari-

son. Moreover, in some cases (e.g., excitation energies or

frequencies) the absolute position on the energy range is

often not available with sufficient precision due to the difficul-

ties involved in accurate computations of QM data, while the

overall spectra profile is usually well reproduced. For that rea-

son, it is often necessary to shift theoretical spectra on the

energy range, to compare more properly experimental and

theoretical results. This task is facilitated by a number of inter-

active tools, which allow runtime manipulation of spectra posi-

tions and intensities, the latter option (alternative to simple

normalization) being particularly useful if regions other than

spectra maxima are of interest. Finally VMS-Draw allows also

plotting differences between pairs of spectra, to easily mark

best matching features and largest discrepancies between

them.

As a final comment, let us recall that, whenever normal

modes are available in a Gaussian output file, they can be

shown at runtime by using a dedicated menu (see Fig. 8) and

the same applies to molecular orbitals (see Fig. 9).

Vibrational Spectra

The calculations of vibrational spectra for molecular systems

usually rely on the so-called double harmonic approxima-

tion,[30,31] in which the potential energy surface (PES) is

expanded in a Taylor series about the equilibrium geometry

Figure 3. Main Possibilities Offered by VMS-Draw for spectra manipulation

and analysis. [Color figure can be viewed in the online issue, which is avail-

able at wileyonlinelibrary.com.]

Figure 4. Electronic spectra of different substitued p-Phenylene bis-imidazoles collected in the same frame. [Color figure can be viewed in the online issue,

which is available at wileyonlinelibrary.com.]



http://wileyonlinelibrary.com


up to second order, and the electric dipole moment (for Infra-

Red, IR), magnetic dipole moment [for vibrational circular

dichroism, (VCD)], and electronic polarizability (for Raman), are

also expanded in Taylor series truncated after the first order.

At this level of approximation vibrational spectra can be inter-

preted in terms of normal modes and vibrational frequencies,

and well-known selection rules can be derived. One such rule

demands that only one normal mode is excited at a time, and

that its quantum vibrational number can change only by 61.

If a system is initially in the ground vibrational state, this

Figure 5. Absorbance IR spectra of three low-energy glycine conformers in the 1000–2000 cm21 range. Single contributions from Ip/ttt, IIn/ccc, IIIp/tct

(upper panel), and total spectrum obtained as a sum of the Ip/ttt, IIn/ccc and IIIp/tct contributions weighted for relative abundances (see Ref. [28]) (lower

panel). [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

Figure 6. Normalized absorption (blue) and emission (red) electronic spectra of Me-Phenylene bis-imidazoles. [Color figure can be viewed in the online

issue, which is available at wileyonlinelibrary.com.]






implies that the spectrum will only present fundamental

bands, all other transitions having vanishing intensities.

It is well-known (see, e.g., Refs. [31–34]) that neglecting the

effects of mechanical and electrical anharmonicity can yield

substantial errors in the calculation of positions and heights of

the different peaks. The lack of overtones and combination

bands in the calculated spectra is especially troublesome as it

precludes the exploration of several spectral regions. To over-

come those limitations, one of us has implemented in the

Gaussian package second-order vibrational perturbation theory

Figure 7. Comparison between vibrationally resolved computed (red) and experimental (blue) absorption electronic spectra of dideprotonated alizarin

along with the scheme of plot digitisation procedure. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

Figure 8. VMS-Draw screenshot with the harmonic IR spectrum of ferrocene. The possibility to show normal modes and to write annotations directly on

the spectrum is evidenced. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]





(VPT2) for both frequencies and intensities.[30,34–39] This

approach produces much more realistic results, but this comes

at the price of increased complexity of the resulting spectrum

because of the greatly increased number of peaks. After com-

putation of all peak positions and intensities, any meaningful

comparison with experimental data requires the convolution

of each peak with a line-shape function (usually a Gaussian or

a Lorentzian), with a half width at half maximum (HWHM) cho-

sen to give the best-fit of experimental data. This often

requires some trial and error, and an interactive GUI able to

perform such adjustments and to plot the resulting spectra in

real time is very useful.

Whenever a Gaussian output file is opened, VMS-Draw is

able to compare a reference experimental spectrum with its

computed harmonic and/or anharmonic counterparts. Selec-

tion of each peak in the stick spectrum directly provides its

assignment to a specific transition, and also the HWHM of the

convoluted spectrum can be easily adjusted. IR spectra can be

converted from Absorbance A (which is proportional to the

molar extinction coefficient �, a quantity provided by several

ESCs) to Transmittance T, which is the de-facto standard in

experimental reports, using the well-known relation A52log T .

The computed quantity is �, therefore, due to the Beer-

Lambert law, this conversion requires, in principle, knowledge

of the sample concentration and of the length of the optical

path; therefore, to avoid any inconsistency, VMS-Draw provides

the Transmittance spectrum in arbitrary units. In the case of

Raman spectra the treatment is more involved, since ESCs usu-

ally produce the Raman activity Ai, whereas the primary exper-

imental observable is the Raman cross-section. The relation

between the two quantities is

r0i 510248Na 2pðmx2miÞð Þ4 Ai

45

where i refer to a given normal mode, r0 is the cross-section

in cm2 sr21 mol21, Na is Avogadro’s number, mx is the incident

Figure 9. Graphical representation of the molecular orbitals of OMe-

Phenylene bis-imidazole. [Color figure can be viewed in the online issue,


Figure 10. Computed (Harmonic and Anharmonic) and experimental IR

spectra of nicotine in chloroform solution. [Color figure can be viewed in

the online issue, which is available at wileyonlinelibrary.com.]

Figure 11. Computed (harmonic and anharmonic) VCD spectrum of nico-

tine in chloroform solution. The two bottom panels show nonfundamental

transitions in the anharmonic spectrum. The intensity of the VCD spectrum

is reported in km mol21. [Color figure can be viewed in the online issue,








frequency in cm21, mi the energy of the transition in cm21,

and Ai is the Raman activity in A6.

VMS-Draw can convert the spectrum between different rep-

resentations and plot both the Raman activity and the Raman

cross-section. In particular, comparison of harmonic or anhar-

monic simulated spectra with their experimental counterparts

can be performed by plotting the Raman cross-section and

adjusting the HWHM and line-shape function of the peaks.

Figure 10 shows, as an example, the comparison between the

harmonic, anharmonic, and experimental IR spectra of nicotine in

chloroform solution.[40] The stick-spectra are superposed to the

convoluted ones, allowing for an easier assignment of the experi-

mental bands since clicking on a peak shows the nature of each

excitation. Figure 11 shows the VCD spectrum of nicotine in chlo-

roform solution. Also in this case, there is a strong difference

between the harmonic and anharmonic spectra, especially

because the latter include also nonfundamental bands. As an

example, the two overtone regions ([1200, 2000] and [4000,

6000] cm21) of the spectrum have been expanded and plotted

in the lower panels of Figure 11. At the harmonic level all over-

tones have vanishing intensity, therefore, both regions of the

spectrum would be completely precluded.

In addition to spectra visualization, other tools are available to

analyze in detail the outcome of anharmonic computations. The

contribution of the higher derivatives to the anharmonic frequen-

cies are collected in the so called X matrix, which can be split into

different submatrices[34,37] (containing Coriolis, cubic and quartic

terms, respectively). Furthermore, the anharmonic correction for

each mode can be split into intrinsic anharmonicity, direct coupling

with other normal modes, and indirect coupling with more than

Figure 12. Heat diagram describing couplings between normal modes (from Kiij matrix) of glycine. The strongly coupled NH2 symmetric and CH2 asymmet-

ric stretching are highlighted by arrows. Fully anharmonic (24 modes) and reduced dimensionality (only 5 high-frequency modes) computed spectra are

also shown with the absolute IR intensities in km mol21. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]




one additional mode. The first two contributions are collected in

the diagonal and off-diagonal elements of the Y matrix, respectively.

All those matrices can be visualized within VMS-Draw as heat maps,

where the darkness of the color increases with the magnitude of

the matrix element, using linear or logarithmic scales. The analysis is

further facilitated by the possibility of zooming (important for larger

systems) or highlighting all elements larger than a preselected

threshold. Analysis of anharmonic couplings provides important

information on the system under study and can be also used for

defining cost-effective reduced-dimensionality anharmonic mod-

els.[31,41] An analysis of the cubic force constants allows to improve

the choice of the normal modes whose anharmonicity can be safely

neglected to reach a given accuracy (see Fig. 12).

Electronic Spectra

One photon absorption and emission (OPA and OPE, respec-

tively) spectra together with their chiral counterparts [elec-

tronic circular dichroism, (ECD), and circularly polarized

luminescence, (CPL), respectively] involve transitions between

vibrational energy levels of two different electronic states.

However, due to the different time scales of electron and

nuclear motion, the so called Franck–Condon approximation

(stating that electronic transition occurs in such a short time

that the nuclei remain fixed)[42,43] is often satisfactory. Thus, to

a first approximation, electronic transitions can be represented

in terms of differences in electron densities and energies

between initial and final electronic states, that is, by vertical

electronic excitations (VEE) with the corresponding transition

dipole moments (OPA spectra) or rotatory strengths (ECD

spectra). Within the VEE framework simulated stick spectra are

further convoluted (usually by Gaussian functions with large

HWHM) to simulate the broadening of experimental spectra.

For longer time scales, the changes in electron density lead

to geometry relaxation and, as a consequence, to changes of

vibrational properties, dipole moments, and so forth. The

energy difference between excited and ground electronic

states at their respective equilibrium geometries is called adia-

batic excitation energy, while the “0-0” or “origin” transition

energy is obtained by considering also the difference of zero

point vibrational energies. Finally, vertical emission spectra are

obtained from energy differences between excited and ground

state at the equilibrium geometry of the former. To visualize

geometry changes accompanying electronic excitations, a tool

Figure 13. Single excitation spectrum with oscillator strengths of CN-Phenylene bis-imidazole (middle panel). Geometries of Initial (Red) and Final (blue)

State are reported in the upper panel. Contribution of one-electron transitions (percentages) to the OPA spectrum is reported in the lower panel. [Color

figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]





has been set up, which superposes simplified stick and ball

models of the equilibrium geometries of ground and excited

states drawn in different colors (upper panel of Fig. 13).

Concerning the post-treatment of spectroscopic simulations,

to the best of our knowledge, none of the available all-in-one

packages is flexible enough to process the rich information

produced by ESCs for excited electronic states. For this reason,

VMS-Draw has been designed to include several other post-

processing tools, including, of course, the plot of both the

convoluted and nonconvoluted bands of a vertical excitation

or emission spectrum, each corresponding to specific elec-

tronic transitions (middle panel of Fig. 13). The convoluted

spectrum might be tuned using the HWHM criterion and then

expressed in different units (eV, nm, or cm21). In addition to

this standard feature, a specific tool allows to express each

overall electronic transition in terms of the percentages of spe-

cific configurations (labeled by the hole and particle difference

with respect to the ground state) directly with a histogram

(lower panel of Fig. 13). Such a graphical representation simpli-

fies comparison between the characteristics of electronic tran-

sitions for set of different geometries, or the following of a

specific excited state along reaction paths.[44] It is also possible

to export the data into a dedicated file, which gives the transi-

tion composition along with the oscillator strength and the

excitation energy/wavelength. The default threshold (10%) for

representing a state contribution is usually satisfactory, but

can, of course, be manually tuned to adjust the number of

transitions reported in the histogram and in the exported file.

Furthermore, when only a reduced set of excitations is of inter-

est, the user has the possibility to tune the number of transi-

tions to be depicted.

The actual bandshape of electronic transitions is determined

by vibronic contributions, which may result in a vibrationally

resolved spectrum or more simply in a nonsymmetrical band-

shape, which cannot be reproduced by a simple Gaussian or

Lorentzian function.[45] To compute realistic electronic spectra

line-shapes, different models are available.[46]

In particular, it is possible to compute vibrationally resolved

OPA, OPE, ECD, and CPL spectra with the inclusion of mode-

mixing (Duschinsky) effects for the treatment of the excited-

state PES, and of Herzberg-Teller contributions in the Taylor

expansions of the transition electric and magnetic dipole

moments.[47,48]

Contrary to what happens in the case of vibrational spectra,

the number of possible vibronic transitions is not limited by

selection rules and may well approach hundreds of millions to

obtain converged spectra. For that reason the assignment

information is printed only for the transitions whose intensity

exceeds a given threshold, which can be modified by the user.

However, the stick or convoluted spectrum is fully printed in

the output file and can be easily plotted possibly including

convolution with suitable broadening functions. In analogy

with vibrational spectra, it is also possible, by clicking on a

specific peak, to see the initial and final vibronic states

involved in the corresponding transition. Furthermore, stick

and convoluted spectra are superposed to aid the comparison

with experimental data. An estimation of spectrum conver-

gence is also given, based on analytical sum rules. As men-

tioned above, both vibrational frequencies and normal modes

can be different in the two electronic states. The resulting

mode-mixing can be expressed in terms of a linear transforma-

tion between both sets of modes, one for the ground (Q0) and

one for the excited (Q00) state[49]:

Q005JQ01K

In the above equation J is the so-called Duschinsky matrix

(mode rotation) and K is the shift vector. Analysis of the

Duschinsky matrix provides useful information about the mixing

of the vibrational modes caused by the electronic excitation,

while the shift vector is related to the change in the equilibrium

geometry between the two states expressed in terms of normal

modes. VMS-Draw is able to read both set of data from the

same output file containing the spectrum, and plot them to

grasp the magnitude of such effects and easily relate them to

the spectrum itself. This analysis is further aided by the possibil-

ity to plot and compare the equilibrium structures for both

states, as shown in the upper panel of Figure 13.

In Figure 14, we show, as an example, the electronic spectra

of Alizarin-Al(III) complex in the 200–600 nm (UV-vis) region.[50]

Let us start, for purposes of illustration, from a rough overall

picture, based on the computation of vertical transitions

(shown in the upper panel), which, together with an analysis

of the composition of electronic transitions, allows to select

the excited states to be examined in deeper detail. Once the

electronic transitions of interest are selected, vibronic compu-

tations with a suitably chosen model (here Vertical Gradient,

see Refs. [47,48] for detailed account) can be performed. The

vibrationally resolved absorption spectrum of alizarin-Al(III),

includes non-negligible contributions from the first seven

bright states (S1, S2, S4, S5, S6, S8, and S11). This kind of plot

can be obtained by opening all seven output files from each

vibronic calculation at the same time, and VMS-Draw will place

all the graphs within the same window, allowing the user to

visualize all the contributions at the same time (middle panel)

as well as the full absorption spectrum obtained as a sum of

single-state contributions (lower panel). The full vibronic spec-

trum can be also easily compared with the one based on verti-

cal electronic transitions (upper and lower panel respectively).

As mentioned above, further information concerning the

vibronic contributions can be obtained (see Fig. 15), including

Duschinsky matrix, Shift Vector (in terms of the normal modes

of the initial state) as well as spectrum convergence by includ-

ing higher-order transitions.

Specific tools for electronic spectra are completed by the

possibility of evaluating the color of a molecular system taking

into account that the band shape in the visible spectral range

(380–780 nm) is directly responsible for the color perceived by

the human eye. The CIE color coordinates are obtained calcu-

lating the spectral overlap with the standard CIE Red, Green,

and Blue color matching functions,[51,52] and are then con-

verted into RGB color models suitable for a digital display. This

feature can be used, for instance, for the study of environmen-

tal factors responsible for the aging and color modification of



ancient pigments or for the prediction of the color of new

synthetic dyes. Both the red color predictet for Alizarin-Al(III)

complex (shown as a red circle in the lower panel of Figure 1)

and the orange coloration issuing from an analogous simula-

tion for the Alizarin-Mg(II) complex are in line with

experiment.[50]

Although RR is, in principle, a vibrational spectroscopy, the

underlying theory and computational machinery are closer to

those of the vibrationally resolved electronic spectra dis-

cussed in this section.[53–55] As a matter of fact, RR spectra

resemble their non resonant counterparts, but with strongly

enhanced intensities and additional modulation by vibronic

Figure 14. Electronic absorption spectrum of alizarin-Al(III). Upper panel: spectrum based on vertical transitions and its convolution with Gaussian functions

(HWHM of 2000 cm21). Middle panel: single state vibronic transitions, stick spectra and their convolution with Gaussian functions (HWHM of 500 cm21).

Lower panel: final vibronic spectrum obtained from convolution with Gaussian functions (HWHM of 500 cm21) and underlying stick spectrum. The final

computed color is also shown (see text for details). [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

Figure 15. Analysis of vibrationally resolved electronic spectra. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]






interactions with one or more excited electronic states lead

in resonance by the applied laser radiation. As a conse-

quence, customary Raman selection rules are no longer valid.

The RR spectrum of a system can be recorded (and com-

puted) for different incident frequencies, so that a 3D plot

showing the dependence of the absorption on both the

Raman shift (on the X axis) and the incident frequency (on

the Y axis) could be more informative. VMS-Draw is able to

perform the convolution of each stick spectrum and also the

interpolation along the incident frequency axis producing

either a 2D heat map or a 3D plot. An example of 3D spec-

trum is shown in Figure 16.

Microwave and Electron Spin ResonanceSpectra

In all the cases discussed above, the primary information issu-

ing from electronic computations is processed by specific links

of the Gaussian package (our reference VMS-Comp module) so

that all the data needed by VMS-Draw are taken from the out-

put file(s). The situation is different for MW and ESR spectra,

which require further computations after the generation of

vibro-rotational terms and/or hyperfine tensors by Gaussian.

Although our final goal is to develop simulations of these

spectra within other new links of the Gaussian code, for the

time being we use for MW spectra the SPCAT code,[56] which

has been compiled for different platforms and operating sys-

tems and interfaced to Gaussian from one side (to obtain

directly dipole moments, vibro-rotational constants, etc.) and

to VMS-Draw to simplify the creation of the other complicated

input files required by the original version and to manage the

computed spectra in the same easy and flexible way as

described above for other spectroscopies. An example of MW

spectrum is given in Figure 17. For ESR spectra, time-scale sep-

aration allows essentially ab initio simulations by feeding into

the stochastic Liouville equation (SLE) magnetic tensors (possi-

bly including vibrational averaging effects) computed by ESCs

together with diffusion tensors obtained using structural

parameters issuing from the same ESCs and finite-element dis-

cretizations.[4] This task is performed by the E-SpiReS (Electron

Spin Resonance Simulations) code,[57] which takes from

Figure 16. RR spectrum of chlorophyll a1 as a function of both Raman shift

(X axis) and incident frequency (Y axis) cm21. [Color figure can be viewed

in the online issue, which is available at wileyonlinelibrary.com.]

Figure 17. Calculated rotational spectrum of water, upper panel and electron spin resonance spectrum of tempone (4-Oxo-2,2,6,6-tetramethyl-1-piperidiny-

loxy radical), lower panel. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]





Gaussian output files the necessary structural data and mag-

netic tensors, computes diffusion tensors and, next, solves the

SLE. E-SpiReS can be directly operated by the VMS-Draw GUI

and its outputs are managed now in full analogy with those

of the other spectra discussed above. An example of ESR spec-

trum is given in the lower panel of Figure 17.

Conclusion

We have presented a new GUI, purposely tailored for computa-

tional spectroscopy, which includes, together all conventional

features, several advanced tools allowing user-friendly applica-

tions for both routine and more advanced studies taking into

account also spectra manipulation and comparison with experi-

mental data. From a technical point of view, particular attention

has been devoted to robustness, generality and portability

onto different platforms. Furthermore, the definition of quite

general classes of data allows the use of VMS-Draw with most

ESCs. At the same time, a particularly effective automatic inter-

face is already integrated for the Gaussian code. Although

VMS-Draw is intended for all kinds of spectroscopies, the

selected examples refer in particular to vibrational, electronic,

and vibronic spectra. Here, specific features of VMS-Draw, like

full support for anharmonic frequencies and intensities, or

advanced features for spectra manipulation can be particularly

useful for both nonspecialists and more experienced users.

Planned future extensions include addition of other spectros-

copies like NMR, representation of different surfaces (isodensity,

spin-density, etc.) and better integration with the major ESCs.

However, also pending these further developments, we think

that VMS-Draw can already represent a useful additional tool

for spectroscopic studies integrating measurements and com-

puter simulations.

Acknowledgments

The research leading to these results has received funding from the

European Union’s Seventh Framework Programme (FP7/2007-2013)

under grant agreement No. ERC-2012-AdG-320951-DREAMS. The

authors gratefully thank the high performance computer facilities

of the DREAMS center (http://dreamshpc.sns.it) for providing com-

puter resources. The support of the COST CMTS-Action CM1002

“COnvergent Distributed Environment for Computational Spectros-

copy (CODECS)” is also acknowledged.

Keywords: electronic spectroscopy � vibrational spectrosco-

py � vibronic spectroscopy � graphical user interface � virtual

multifrequency spectrometer

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Received: 17 September 2014Accepted: 12 October 2014Published online on 00 Month 2014



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